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Publications 2020

Direct Collaborations

Genome-wide repeat expansions in complex disorders: beyond the coding sequence
Yuen R. Nov 2020. CSBio2020: CSBio '20: Proceedings of the Eleventh International Conference on Computational Systems-Biology and Bioinformatics. doi:10.1145/3429210.3429231

Association of IGF1 and VEGFA polymorphisms with diabetic retinopathy in Pakistani population
Khan N, Paterson AD, Roshandel D, Raza A, Ajmal M, Waheed NK, Azam M, Qamar R. Acta Diabetol. 2020 Feb;57(2):237-245. doi: 10.1007/s00592-019-01407-5. Epub 2019 Aug 31 PubMed PMID: 31473834

Synaptic dysfunction in human neurons with autism-associated deletions in PTCHD1-AS
Ross PJ, Zhang WB, Mok RSF, Zaslavsky K, Deneault E, D'Abate L, Rodrigues DC, Yuen RKC, Faheem M, Mufteev M, Piekna A, Wei W, Pasceri P, Landa RJ, Nagy A, Varga B, Salter MW, Scherer SW, Ellis J. Biol Psychiatry. 2020 Jan 15;87(2):139-149. doi: 10.1016/j.biopsych.2019.07.014. Epub 2019 Jul 29 PubMed PMID: 31540669. PubMed Central PMCID: PMC6948145

VikNGS: a C++ variant integration kit for next generation sequencing association analysis
Baskurt Z, Mastromatteo S, Gong J, Wintle RF, Scherer SW, Strug LJ. Bioinformatics. 2020 Feb 15;36(4):1283-1285. doi: 10.1093/bioinformatics/btz716. PubMed PMID: 31580400. PubMed Central PMCID: PMC7703770

Passos- Bueno MR. Meta-analyses support previous and novel autism candidate genes: outcomes of an unexplored Brazilian cohort
da Silva Montenegro EM, Costa CS, Campos G, Scliar M, de Almeida TF, Zachi EC, Silva IMW, Chan AJS, Zarrei M, Lourenço NCV, Yamamoto GL, Scherer S. Autism Res. 2020 Feb;13(2):199-206. doi: 10.1002/aur.2238 Epub 2019 Nov 6. PubMed PMID: 31696658

Refining critical regions in 15q24 microdeletion syndrome pertaining to autism
Liu Y, Zhang Y, Zarrei M, Dong R, Yang X, Zhao D, Scherer SW, Gai Z. Am J Med Genet B Neuropsychiatr Genet. 2020 Jun;183(4):217-226. doi: 10.1002/ajmg.b.32778. Epub 2020 Jan 18. PubMed PMID: 31953991

Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion
Cleynen I, Engchuan W, Hestand MS, Heung T, Holleman AM, Johnston HR, Monfeuga T, McDonald-McGinn DM, Gur RE, Morrow BE, Swillen A, Vorstman JAS, Bearden CE, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, Warren ST, Owen MJ, Chopra P, Cutler DJ, Duncan R, Kotlar AV, Mulle JG, Voss AJ, Zwick ME, Diacou A, Golden A, Guo T, Lin JR, Wang T, Zhang Z, Zhao Y, Marshall C, Merico D, Jin A, Lilley B, Salmons HI, Tran O, Holmans P, Pardinas A, Walters JTR, Demaerel W, Boot E, Butcher NJ, Costain GA, Lowther C, Evers R, van Amelsvoort TAMJ, van Duin E, Vingerhoets C, Breckpot J, Devriendt K, Vergaelen E, Vogels A, Crowley TB, McGinn DE, Moss EM, Sharkus RJ, Unolt M, Zackai EH, Calkins ME, Gallagher RS, Gur RC, Tang SX, Fritsch R, Ornstein C, Repetto GM, Breetvelt E, Duijff SN, Fiksinski A, Moss H, Niarchou M, Murphy KC, Prasad SE, Daly EM, Gudbrandsen M, Murphy CM, Murphy DG, Buzzanca A, Fabio FD, Digilio MC, Pontillo M, Marino B, Vicari S, Coleman K, Cubells JF, Ousley OY, Carmel M, Gothelf D, Mekori Domachevsky E, Michaelovsky E, Weinberger R, Weizman A, Kushan L, Jalbrzikowski M, Armando M, Eliez S, Sandini C, Schneider M, Béna FS, Antshel KM, Fremont W, Kates WR, Belzeaux R, Busa T, Philip N, Campbell LE, McCabe KL, Hooper SR, Schoch K, Shashi V, Simon TJ, Tassone F, Arango C, Fraguas D, García- Miñaúr S, Morey-Canyelles J, Rosell J, Suñer DH, Raventos-Simic J; International 22q11.2DS Brain and Behavior Consortium, Epstein MP, Williams NM, Bassett AS. Mol Psychiatry. 2020 Feb 3:10.1038/s41380-020-0654-3. doi: 10.1038/s41380-020-0654-3. PubMed PMID: 32015465. PubMed Central PMCID: PMC7396297

The Cardiac Genome Clinic: implementing genome sequencing in pediatric heart disease
Reuter MS, Chaturvedi RR, Liston E, Manshaei R, Aul RB, Bowdin S, Cohn I, Curtis M, Dhir P, Hayeems RZ, Hosseini SM, Khan R, Ly LG, Marshall CR, Mertens L, Okello JBA, Pereira SL, Raajkumar A, Seed M, Thiruvahindrapuram B, Scherer SW, Kim RH, Jobling RK. Genet Med. 2020 Jun;22(6):1015-1024. doi: 10.1038/s41436-020-0757-x. Epub 2020 Feb 10. PubMed PMID: 32037394. PubMed Central PMCID: PMC7272322

Shared genetic risk between eating disorder- and substance-use-related phenotypes: evidence from genome-wide association studies
Munn-Chernoff MA, Johnson EC, Chou YL, Coleman JRI, Thornton LM, Walters RK, Yilmaz Z, Baker JH, Hübel C, Gordon S, Medland SE, Watson HJ, Gaspar HA, Bryois J, Hinney A, Leppä VM, Mattheisen M, Ripke S, Yao S, Giusti-Rodríguez P, Hanscombe KB, Adan RAH, Alfredsson L, Ando T, Andreassen OA, Berrettini WH, Boehm I, Boni C, Boraska Perica V, Buehren K, Burghardt R, Cassina M, Cichon S, Clementi M, Cone RD, Courtet P, Crow S, Crowley JJ, Danner UN, Davis OSP, de Zwaan M, Dedoussis G, Degortes D, DeSocio JE, Dick DM, Dikeos D, Dina C, Dmitrzak-Weglarz M, Docampo E, Duncan LE, Egberts K, Ehrlich S, Escaramís G, Esko T, Estivill X, Farmer A, Favaro A, Fernández-Aranda F, Fichter MM, Fischer K, Föcker M, Foretova L, Forstner AJ, Forzan M, Franklin CS, Gallinger S, Giegling I, Giuranna J, Gonidakis F, Gorwood P, Gratacos Mayora M, Guillaume S, Guo Y, Hakonarson H, Hatzikotoulas K, Hauser J, Hebebrand J, Helder SG, Herms S, Herpertz-Dahlmann B, Herzog W, Huckins LM, Hudson JI, Imgart H, Inoko H, Janout V, Jiménez-Murcia S, Julià A, Kalsi G, Kaminská D, Karhunen L, Karwautz A, Kas MJH, Kennedy JL, Keski-Rahkonen A, Kiezebrink K, Kim YR, Klump KL, Knudsen GPS, La Via MC, Le Hellard S, Levitan RD, Li D, Lilenfeld L, Lin BD, Lissowska J, Luykx J, Magistretti PJ, Maj M, Mannik K, Marsal S, Marshall CR, Mattingsdal M, McDevitt S, McGuffin P, Metspalu A, Meulenbelt I, Micali N, Mitchell K, Monteleone AM, Monteleone P, Nacmias B, Navratilova M, Ntalla I, O'Toole JK, Ophoff RA, Padyukov L, Palotie A, Pantel J, Papezova H, Pinto D, Rabionet R, Raevuori A, Ramoz N, Reichborn-Kjennerud T, Ricca V, Ripatti S, Ritschel F, Roberts M, Rotondo A, Rujescu D, Rybakowski F, Santonastaso P, Scherag A, Scherer SW, Schmidt U, Schork NJ, Schosser A, Seitz J, Slachtova L, Slagboom PE, Slof-Op't Landt MCT, Slopien A, Sorbi S, Światkowska B, Szatkiewicz JP, Tachmazidou I, Tenconi E, Tortorella A, Tozzi F, Treasure J, Tsitsika A,Tyszkiewicz-Nwafor M, Tziouvas K, van Elburg AA, van Furth EF, Wagner G, Walton E, Widen E, Zeggini E, Zerwas S, Zipfel S, Bergen AW, Boden JM, Brandt H, Crawford S, Halmi KA, Horwood LJ, Johnson C, Kaplan AS, Kaye WH, Mitchell J, Olsen CM, Pearson JF, Pedersen NL, Strober M, Werge T, Whiteman DC, Woodside DB, Grove J, Henders AK, Larsen JT, Parker R, Petersen LV, Jordan J, Kennedy MA, Birgegård A, Lichtenstein P, Norring C, Landén M, Mortensen PB, Polimanti R, McClintick JN, Adkins AE, Aliev F, Bacanu SA, Batzler A, Bertelsen S, Biernacka JM, Bigdeli TB, Chen LS, Clarke TK, Degenhardt F, Docherty AR, Edwards AC, Foo JC, Fox L, Frank J, Hack LM, Hartmann AM, Hartz SM, Heilmann-Heimbach S, Hodgkinson C, Hoffmann P, Hottenga JJ, Konte B, Lahti J, Lahti-Pulkkinen M, Lai D, Ligthart L, Loukola A, Maher BS, Mbarek H, McIntosh AM, McQueen MB, Meyers JL, Milaneschi Y, Palviainen T, Peterson RE, Ryu E, Saccone NL, Salvatore JE, Sanchez-Roige S, Schwandt M, Sherva R, Streit F, Strohmaier J, Thomas N, Wang JC, Webb BT, Wedow R, Wetherill L, Wills AG, Zhou H, Boardman JD, Chen D, Choi DS, Copeland WE, Culverhouse RC, Dahmen N, Degenhardt L, Domingue BW, Frye MA, Gäebel W, Hayward C, Ising M, Keyes M, Kiefer F, Koller G, Kramer J, Kuperman S, Lucae S, Lynskey MT, Maier W, Mann K, Männistö S, Müller-Myhsok B, Murray AD, Nurnberger JI, Preuss U, Räikkönen K, Reynolds MD, Ridinger M, Scherbaum N, Schuckit MA, Soyka M, Treutlein J, Witt SH, Wodarz N, Zill P, Adkins DE, Boomsma DI, Bierut LJ, Brown SA, Bucholz KK, Costello EJ, de Wit H, Diazgranados N, Eriksson JG, Farrer LA, Foroud TM, Gillespie NA, Goate AM, Goldman D, Grucza RA, Hancock DB, Harris KM, Hesselbrock V, Hewitt JK, Hopfer CJ, Iacono WG, Johnson EO, Karpyak VM, Kendler KS, Kranzler HR, Krauter K, Lind PA, McGue M, MacKillop J, Madden PAF, Maes HH, Magnusson PKE, Nelson EC, Nöthen MM, Palmer AA, Penninx BWJH, Porjesz B, Rice JP, Rietschel M, Riley BP, Rose RJ, Shen PH, Silberg J, Stallings MC, Tarter RE, Vanyukov MM, Vrieze S, Wall TL, Whitfield JB, Zhao H, Neale BM, Wade TD, Heath AC, Montgomery GW, Martin NG, Sullivan PF, Kaprio J, Breen G, Gelernter J, Edenberg HJ, Bulik CM, Agrawal A. Addict Biol. 2021 Jan;26(1):e12880. doi: 10.1111/adb.12880. Epub 2020 Feb 16. PubMed PMID: 32064741. PubMed Central PMCID: PMC7429266

Perceived utility of biological testing for autism spectrum disorder is associated with child and family functioning
Yusuf A, Peltekova I, Savion-Lemieux T, Frei J, Bruno R, Joober R, Howe J, Scherer SW, Elsabbagh M. Res Dev Disabil. 2020 May;100:103605. doi: 10.1016/j.ridd.2020.103605. Epub 2020 Feb 28. PubMed PMID: 32120048

DNA methylation signature for EZH2 functionally classifies sequence variants in three PRC2 complex genes
Choufani S, Gibson WT, Turinsky AL, Chung BHY, Wang T, Garg K, Vitriolo A, Cohen ASA, Cyrus S, Goodman S, Chater-Diehl E, Brzezinski J, Brudno M, Ming LH, White SM, Lynch SA, Clericuzio C, Temple IK, Flinter F, McConnell V, Cushing T, Bird LM, Splitt M, Kerr B, Scherer SW, Machado J, Imagawa E, Okamoto N, Matsumoto N, Testa G, Iascone M, Tenconi R, Caluseriu O, Mendoza-Londono R, Chitayat D, Cytrynbaum C, Tatton-Brown K, Weksberg R. Am J Hum Genet. 2020 May 7;106(5):596-610. doi: 10.1016/j.ajgh.2020.03.008. Epub 2020 Apr 2. PubMed PMID: 32243864. PubMed Central PMCID: PMC7212265

Ancestry and frequency of genetic variants in the general population are confounders in the characterization of germline variants linked to cancer
Bobyn A, Zarrei M, Zhu Y, Hoffman M, Brenner D, Resnick AC, Scherer SW, Gallo M. BMC Med Genet. 2020 May 6;21(1):92. doi: 10.1186/s12881-020-01033-x. PubMed PMID: 32375678. PubMed Central PMCID: PMC7201963

Segregating patterns of copy number variations in extended autism spectrum disorder (ASD) pedigrees
Woodbury-Smith M, Zarrei M, Wei J, Thiruvahindrapuram B, O'Connor I, Paterson AD, Yuen RKC, Dastan J, Stavropoulos DJ, Howe JL, Thompson A, Parlier M, Fernandez B, Piven J, Anagnostou E, Scherer SW, Vieland VJ, Szatmari P. Am J Med Genet B Neuropsychiatr Genet. 2020 Jul;183(5):268-276. doi: 10.1002/ajmg.b.32785. Epub 2020 May 6. PubMed PMID: 32372567

Genome-wide association study of emotional empathy in children
Woodbury-Smith MR, Paterson AD, Szatmari P, Scherer SW. Sci Rep. 2020 May 4;10(1):7469. doi: 10.1038/s41598-020-62693-06. PubMed PMID: 32366958. PubMed Central PMCID: PMC7198552

Editorial: Secondary vs. Idiopathic Autism
Casanova MF, Casanova EL, Frye RE, Baeza-Velasco C, LaSalle JM, Hagerman RJ, Scherer SW, Natowicz MR. Front Psychiatry. 2020 Apr 14;11:297. doi: 10.3389/fpsyt.2020.00297. eCollection 2020. PubMed PMID: 3246372. PubMed Central PMCID: PMC7171716

ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Dolzhenko E, Bennett MF, Richmond PA, Trost B, Chen S, van Vugt JJFA, Nguyen C, Narzisi G, Gainullin VG, Gross AM, Lajoie BR, Taft RJ, Wasserman WW, Scherer SW, Veldink JH, Bentley DR, Yuen RKC, Bahlo M, Eberle MA. Genome Biol. 2020 Apr 28;21(1):102. doi: 10.1186/s13059-020-02017-z. PubMed PMID: 32345345. PubMed Central PMCID: PMC7187524

Associations of clinical and inflammatory biomarker clusters with juvenile idiopathic arthritis categories
Rezaei E, Hogan D, Trost B, Kusalik AJ, Boire G, Cabral DA, Campillo S, Chédeville G, Chetaille AL, Dancey P, Duffy C, Duffy KW, Eng SWM, Gordon J, Guzman J, Houghton K, Huber AM, Jurencak R, Lang B, Laxer RM, Morishita K, Oen KG, Petty RE, Ramsey SE, Scherer SW, Scuccimarri R, Spiegel L, Stringer E, Taylor-Gjevre RM, Tse SML, Tucker LB, Turvey SE, Tupper S, Wintle RF, Yeung RSM, Rosenberg AM; BBOP Study Group. Rheumatology (Oxford). 2020 May 1;59(5):1066-1075. doi: 10.1093/rheumatology/kez382. PubMed PMID: 32321162

A framework for an evidence-based gene list relevant to autism spectrum disorder
Schaaf CP, Betancur C, Yuen RKC, Parr JR, Skuse DH, Gallagher L, Bernier RA, Buchanan JA, Buxbaum JD, Chen CA, Dies KA, Elsabbagh M, Firth HV, Frazier T, Hoang N, Howe J, Marshall CR, Michaud JL, Rennie O, Szatmari P, Chung WK, Bolton PF, Cook EH, Scherer SW, Vorstman JAS. Nat Rev Genet. 2020 Jun;21(6):367-376. doi: 10.1038/s41576-020-0231-2. PubMed PMID: 32317787

Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology
Enikanolaiye A, Ruston J, Zeng R, Taylor C, Schrock M, Buchovecky CM, Shendure J, Acar E, Justice MJ. Genome Res. 2020 Apr;30(4):540-552. doi: 10.1101/gr.258400.119. Epub 2020 Apr 21. PubMed PMID: 32317254. PubMed Central PMCID: PMC7197480

DNA methylation age calculators reveal association with diabetic neuropathy in type 1 diabetes
Roshandel D, Chen Z, Canty AJ, Bull SB, Natarajan R, Paterson AD; DCCT/EDIC Research Group. Clin Epigenetics. 2020 Apr 5;12(1):52. doi: 10.1186/s13148-020-00840-06. PubMed PMID: 32248841. PubMed Central PMCID: PMC7132894

A novel intronic variant in UBE3A identified by genome sequencing in a patient with an atypical presentation of Angelman syndrome
Curtis M, Baribeau D, Walker S, Carter M, Costain G, Lamoureux S, Liston E, Marshall CR, Reuter MS, Snell M, Summers J, Vorstman J, Jobling RK. Am J Med Genet A. 2020 Sep;182(9):2145-2151. doi: 10.1002/ajmg.a.61740. Epub 2020 Jul 11. PubMed PMID: 32652832

FARP-1 deletion is associated with lack of response to autism treatment by early start Denver model in a multiplex family
Cucinotta F, Ricciardello A, Turriziani L, Calabrese G, Briguglio M, Boncoddo M, Bellomo F, Tomaiuolo P, Martines S, Bruschetta M, La Fauci Belponer F, Di Bella T, Colombi C, Baccarin M, Picinelli C, Castronovo P, Lintas C, Sacco R, Biederer T, Kellam B, Scherer SW, Persico AM. Mol Genet Genomic Med. 2020 Sep;8(9):e1373. doi: 10.1002/mgg3.1373. Epub 2020 Jun 25. PubMed PMID: 32588496. PubMed Central PMCID: PMC7507005

The Medical Genome Initiative: moving whole-genome sequencing for rare disease diagnosis to the clinic
Marshall CR, Bick D, Belmont JW, Taylor SL, Ashley E, Dimmock D, Jobanputra V, Kearney HM, Kulkarni S, Rehm H; Medical Genome Initiative. Genome Med. 2020 May 27;12(1):48. doi: 10.1186/s13073-020-00748-z. PubMed PMID: 32460895. PubMed Central PMCID: PMC7254704

Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells
Ross PJ, Mok RSF, Smith BS, Rodrigues DC, Mufteev M, Scherer SW, Ellis J. Also acknowledges Janet Buchanan. doi: 10.1186/s13229-020-00333-6. PubMed PMID: 32398033. PubMed Central PMCID: PMC7218542

SARS-CoV-2/COVID-19: viral genomics, epidemiology, vaccines, and therapeutic interventions
Uddin M, Mustafa F, Rizvi TA, Loney T, Suwaidi HA, Al-Marzouqi AHH, Eldin AK, Alsabeeha N, Adrian TE, Stefanini C, Nowotny N, Alsheikh-Ali A, Senok AC. Viruses. 2020 May 10;12(5):526. doi: 10.3390/v12050526. PubMed PMID: 32397688. PubMed Central PMCID: PMC7290442

Multiple early introductions of SARS-CoV-2 into a global travel hub in the Middle East
Tayoun AA, Loney T, Khansaheb H, Ramaswamy S, Harilal D, Deesi ZO, Varghese RM, Al Suwaidi H, Alkhajeh A, AlDabal LM, Uddin M, Hamoudi R, Halwani R, Senok A, Hamid Q, Nowotny N, Alsheikh-Ali A. Sci Rep. 2020 Oct 20;10(1):17720. doi: 10.1038/s41598-020-74666-w. PubMed PMID: 33082405. PubMed Central PMCID: PMC7575574

An exploration of physical and phenotypic characteristics of Bangladeshi children with autism spectrum disorder
Rahaman MA, Lopa M, Uddin KMF, Baqui MA, Keya SP, Faruk MO, Sarker S, Basiruzzaman M, Islam M, AlBanna A, Jahan N, Chowdhury MAKA, Saha N, Hussain M, Colombi C, O'Rielly D, Woodbury-Smith M, Ghaziuddin M, Rahman MM, Uddin M. J Autism Dev Disord. 2020 Sep 25. doi: 10.1007/s10803-020-04703-0. PubMed PMID: 32975665

Predicting the effect of variants on splicing using Convolutional Neural Networks
Thanapattheerakul T, Engchuan W, Chan JH. PeerJ. 2020 Jul 6;8:e9470. doi: 10.7717/peerj.9470. eCollection 2020. PubMed PMID: 32704450. PubMed Central PMCID: PMC7346860

Expanding the search for genetic biomarkers of Parkinson's disease into the living brain
Benoit SM, Xu H, Schmid S, Alexandrova R, Kaur G, Thiruvahindrapuram B, Pereira SL, Jog M, Hebb MO. Neurobiol Dis. 2020 Jul;140:104872 doi: 10.1016/j.nbd.2020.104872. Epub 2020 Apr 14. PubMed PMID: 32302674

Failure to replicate the association of rare loss-of-function variants in type I IFN immunity genes with severe COVID-19
Povysil G, Butler-Laporte G, Shang N, Weng C, Khan A, Alaamery M, Nakanishi T, Zhou S, Forgetta V, Eveleigh R, Bourgey M, Aziz N, Jones S, Knoppers B, Scherer S, Strug L, Lepage P, Ragoussis J, Bourque G, Alghamdi J, Aljawini N, Albes N, Al-Afghani HM, Alghamdi B, Almutair M, Mahmoud ES, Safie LA, Bardisy HE, Harthi FSA, Alshareef A, Suliman BA, Alqahtani S, AlMalik A, Alrashed MM, Massadeh S, Mooser V, Lathrop M, Arabi Y, Mbarek H, Saad C, Al-Muftah W, Badji R, Thani AA, Ismail SI, Gharavi AG, Abedalthagafi MS, Richards JB, Goldstein DB, Kiryluk K. medRxiv [Preprint]. 2020 Dec 21:2020.12.18.20248226. doi: 10.1101/2020.12.18.20248226. PubMed PMID: 33398295. PubMed Central PMCID: PMC7781338

DNA methylation of the oxytocin receptor across neurodevelopmental disorders
Siu MT, Goodman SJ, Yellan I, Butcher DT, Jangjoo M, Grafodatskaya D, Rajendram R, Lou Y, Zhang R, Zhao C, Nicolson R, Georgiades S, Szatmari P, Scherer SW, Roberts W, Anagnostou E, Weksberg R. J Autism Dev Disord. 2021 Jan 4. doi: 10.1007/s10803-020-04792-x. PubMed PMID: 33394241

Statistical power in COVID-19 case-control host genomic study design
Lin YC, Brooks JD, Bull SB, Gagnon F, Greenwood CMT, Hung RJ, Lawless J, Paterson AD, Sun L, Strug LJ; Genetic Epidemiology Committee of the Canadian COVID Genomics Network (CanCOGeN) HostSeq Project. Genome Med. 2020 Dec 28;12(1):115. doi: 10.1186/s13073-020-00818-2. PubMed PMID: 33371892. PubMed Central PMCID: PMC7768597

Phase separation as a missing mechanism for interpretation of disease mutations
Tsang B, Pritišanac I, Scherer SW, Moses AM, Forman-Kay JD. Cell. 2020 Dec 23;183(7):1742-1756. doi: 10.1016/j.cell.2020.11.050. PubMed PMID: 33357399

A distributed whole genome sequencing benchmark study
Corbett RD, Eveleigh R, Whitney J, Barai N, Bourgey M, Chuah E, Johnson J, Moore RA, Moradin N, Mungall KL, Pereira S, Reuter MS, Thiruvahindrapuram B, Wintle RF, Ragoussis J, Strug LJ, Herbrick JA, Aziz N, Jones SJM, Lathrop M, Scherer SW, Staffa A, Mungall AJ. Front Genet. 2020 Dec 1;11:612515. doi: 10.3389/fgene.2020.612515. eCollection 2020. PubMed PMID: 33335541. PubMed Central PMCID: PMC7736078

Linkage analysis identifies an isolated strabismus locus at 14q12 overlapping with FOXG1 syndrome region
Ye XC, Roslin NM, Paterson AD, Lyons CJ, Pegado V, Richmond P, Shyr C, Fornes O, Han X, Higginson M, Ross CJ, Giaschi D, Gregory-Evans C, Patel MS, Wasserman WW. J Med Genet. 2020 Nov 30:jmedgenet-2020-107226. Also acknowledges Illumina microarray genotyping. doi: 10.1136/jmedgenet-2020-107226. PubMed PMID: 33257509

Using common genetic variation to examine phenotypic expression and risk prediction in 22q11.2 deletion syndrome
Davies RW, Fiksinski AM, Breetvelt EJ, Williams NM, Hooper SR, Monfeuga T, Bassett AS, Owen MJ, Gur RE, Morrow BE, McDonald-McGinn DM, Swillen A, Chow EWC, van den Bree M, Emanuel BS, Vermeesch JR, van Amelsvoort T, Arango C, Armando M, Campbell LE, Cubells JF, Eliez S, Garcia-Minaur S, Gothelf D, Kates WR, Murphy KC, Murphy CM, Murphy DG, Philip N, Repetto GM, Shashi V, Simon TJ, Suñer DH, Vicari S, Scherer SW; International 22q11.2 Brain and Behavior Consortium, Bearden CE, Vorstman JAS. Nat Med. 2020 Dec;26(12):1912-1918. doi: 10.1038/s41591-020-1103-1. Epub 2020 Nov 9. PubMed PMID: 33169016. PubMed Central PMCID: PMC7975627

Genes and pathways implicated in Tetralogy of Fallot revealed by ultra-rare variant burden analysis in 231 genome sequences
Manshaei R, Merico D, Reuter MS, Engchuan W, Mojarad BA, Chaturvedi R, Heung T, Pellecchia G, Zarrei M, Nalpathamkalam T, Khan R, Okello JBA, Liston E, Curtis M, Yuen RKC, Marshall CR, Jobling RK, Oechslin E, Wald RM, Silversides CK, Scherer SW, Kim RH, Bassett AS. Front Genet. 2020 Sep 15;11:957. doi: 10.3389/fgene.2020.00957. eCollection 2020. PubMed PMID: 33110418. PubMed Central PMCID: PMC7522597

Genome sequencing identifies a rare case of moderate Zellweger spectrum disorder caused by a PEX3 defect: case report and literature review
Lee W, Costain G, Blaser S, Walker S, Marshall CR, Gonorazky H, Inbar-Feigenberg M. Mol Genet Metab Rep. 2020 Oct 19;25:100664. doi: 10.1016/j.ymgmr.2020.100664. eCollection 2020 Dec. PubMed PMID: 33101983. PubMed Central PMCID: PMC7578253

LocusFocus: web-based colocalization for the annotation and functional follow-up of GWAS
Panjwani N, Wang F, Mastromatteo S, Bao A, Wang C, He G, Gong J, Rommens JM, Sun L, Strug LJ. PLoS Comput Biol. 2020 Oct 22;16(10):e1008336. doi: 10.1371/journal.pcbi.1008336. eCollection 2020 Oct. PubMed PMID: 33090994. PubMed Central PMCID: PMC7608978

First report of t(5;11) KMT2A-MAML1 fusion in de novo infant acute lymphoblastic leukemia
Tandon S, Shago M, Davidson S, Kanwar N, Fuligni F, Shlien A, Whitlock J, Villani A, Abla O. Cancer Genet. 2020 Oct;248-249:31-33. doi: 10.1016/j.cancergen.2020.09.004. Epub 2020 Sep 22. PubMed PMID: 32992102

Does evolution of echolocation calls and morphology in Molossus result from convergence or stasis?
Loureiro LO, Engstrom MD, Lim BK. PLoS One. 2020 Sep 24;15(9):e0238261. doi: 10.1371/journal.pone.0238261. eCollection 2020. PubMed PMID: 32970683. PubMed Central PMCID: PMC7514107

Genome sequencing as a diagnostic test in children with unexplained medical complexity
Costain G, Walker S, Marano M, Veenma D, Snell M, Curtis M, Luca S, Buera J, Arje D, Reuter MS, Thiruvahindrapuram B, Trost B, Sung WWL, Yuen RKC, Chitayat D, Mendoza-Londono R, Stavropoulos DJ, Scherer SW, Marshall CR, Cohn RD, Cohen E, Orkin J, Meyn MS, Hayeems RZ. JAMA Netw Open. 2020 Sep 1;3(9):e2018109. doi: 10.1001/jamanetworkopen.2020.18109. PubMed PMID: 32960281. PubMed Central PMCID: PMC7509619

Adaptation and validation of the Genetic Counseling Outcome Scale for autism spectrum disorders and related conditions
Yusuf A, Peltekova I, Savion-Lemieux T, Frei J, Joober R, Howe J, Scherer SW, Elsabbagh M. J Genet Couns. 2021 Feb; 30(1):305-318. doi: 10.1002/jgc4.1323. Epub 2020 Sep 6. PubMed PMID: 32893416. PubMed Central PMCID: PMC7891368

Genetics of epileptic networks: from focal to generalized genetic epilepsies
Qaiser F, Yuen RKC, Andrade DM. Curr Neurol Neurosci Rep. 2020 Aug 13;20(10):46. doi: 10.1007/s11910-020-01059-x. PubMed PMID: 32789700

Enhancer-gene rewiring in the pathogenesis of Quebec platelet disorder
Liang M, Soomro A, Tasneem S, Abatti LE, Alizada A, Yuan X, Uusküla-Reimand L, Antounians L, Alvi SA, Paterson AD, Rivard GÉ, Scott IC, Mitchell JA, Hayward CPM, Wilson MD. Blood. 2020 Dec 3;136(23):2679-2690. Also acknowledges sequencing facility. doi: 10.1182/blood.2020005394. PubMed PMID: 32663239. PubMed Central PMCID: PMC7735161

DYNC2H1 hypomorphic or retina-predominant variants cause nonsyndromic retinal degeneration
Vig A, Poulter JA, Ottaviani D, Tavares E, Toropova K, Tracewska AM, Mollica A, Kang J, Kehelwathugoda O, Paton T, Maynes JT, Wheway G, Arno G; Genomics England Research Consortium, Khan KN, McKibbin M, Toomes C, Ali M, Di Scipio M, Li S, Ellingford J, Black G, Webster A, Rydzanicz M, Stawinski P, Ploski R, Vincent A, Cheetham ME, Inglehearn CF, Roberts A, Heon E. Genet Med. 2020 Dec;22(12):2041-2051. doi: 10.1038/s41436-020-0915-1. Epub 2020 Aug 5. PubMed PMID: 32753734. PubMed Central PMCID: PMC7708302

TERT promotor variant associated with poor clinical outcome in a patient with novel RBM15-MKL1 fusion-positive pediatric acute megakaryoblastic leukemia
Langenberg-Ververgaert K, Renzi S, Fuligni F, Davidson S, Abdelhaleem M, Lo W, Malkin D, Shlien A, Shago M, Villani A, Abla O. Pediatr Blood Cancer. 2021 Jan;68(1):e28542. doi: 10.1002/pbc.28542. Epub 2020 Aug 2. PubMed PMID: 32743872

CRB1-related retinopathy overlapping the ocular phenotype of S-adenosylhomocysteine hydrolase deficiency
Grudzinska Pechhacker MK, Di Scipio M, Vig A, Tumber A, Roslin N, Tavares E, Vincent A, Hèon E. Ophthalmic Genet. 2020 Oct;41(5):457-464. doi: 10.1080/13816810.2020.1790013. Epub 2020 Jul 20. PubMed PMID: 32689861

Genome-wide detection of tandem DNA repeats that are expanded in autism
Trost B, Engchuan W, Nguyen CM, Thiruvahindrapuram B, Dolzhenko E, Backstrom I, Mirceta M, Mojarad BA, Yin Y, Dov A, Chandrakumar I, Prasolava T, Shum N, Hamdan O, Pellecchia G, Howe JL, Whitney J, Klee EW, Baheti S, Amaral DG, Anagnostou E, Elsabbagh M, Fernandez BA, Hoang N, Lewis MES, Liu X, Sjaarda C, Smith IM, Szatmari P, Zwaigenbaum L, Glazer D, Hartley D, Stewart AK, Eberle MA, Sato N, Pearson CE, Scherer SW, Yuen RKC. Nature. 2020 Oct;586(7827):80-86. doi: 10.1038/s41586-020-2579-z. Epub 2020 Jul 27. PubMed PMID: 32717741


General TCAG, multiple facility, and personal acknowledgments

Maternal obesity persistently alters cardiac progenitor gene expression and programs adult-onset heart disease susceptibility
Ahmed A, Liang M, Chi L, Zhou YQ, Sled JG, Wilson MD, Delgado-Olguín. Mol Metab. 2021 Jan;43:101116. Acknowledges Sergio Pereira. doi: 10.1016/j.molmet.2020.101116. Epub Nov 17. PubMed PMID: 33212270. PubMed Central PMCID: PMC7720025

Determining accurate costs for genomic sequencing technologies-a necessary prerequisite
Jegathisawaran J, Tsiplova K, Hayeems R, Ungar WJ. J Community Genet. 2020 Apr;11(2):235-238. Acknowledges Sergio Pereira, Bhooma Thiruvahindrapuram. doi: 10.1007/s12687-019-00442-7. Epub 2019 Nov 15. PubMed PMID: 31728779. PubMed Central PMCID: PMC7062971

Copy number variation and clinical outcomes in patients with germline PTEN mutations
Yehia L, Seyfi M, Niestroj LM, Padmanabhan R, Ni Y, Frazier TW, Lal D, Eng C. JAMA Netw Open. 2020 Jan 3;3(1):e1920415. Acknowledges TCAG/DGV. doi: 10.1001/jamanetworkopen.2019.20415. PubMed PMID: 32003824. PubMed Central PMCID: PMC7042875

Chromosomal microarray analysis in the investigation of prenatally diagnosed congenital heart disease
Mustafa HJ, Jacobs KM, Tessier KM, Narasimhan SL, Tofte AN, McCarter AR, Cross SN. Am J Obstet Gynecol MFM. 2020 Feb;2(1):100078. Acknowledges TCAG/DGV. doi: 10.1186/s12887-017-0863-3. PubMed PMID: 28472932. PubMed Central PMCID: PMC5418813

Familial infertility (azoospermia and cryptozoospermia) in two brothers-carriers of t(1;7) complex chromosomal rearrangement (CCR): molecular cytogenetic analysis
Olszewska M, Stokowy T, Pollock N, Huleyuk N, Georgiadis A, Yatsenko S, Zastavna D, Yatsenko AN, Kurpisz M. nt J Mol Sci. 2020 Jun 26;21(12):4559. Acknowledges TCAG/DGV. doi: 10.3390/ijms21124559. PubMed PMID: 32604929. PubMed Central PMCID: PMC7349667

High-resolution chromosomal microarray analysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability
Werling AM, Grünblatt E, Oneda B, Bobrowski E, Gundelfinger R, Taurines R, Romanos M, Rauch A, Walitza S. J Neural Transm (Vienna). 2020 Jan;127(1):81-94. Acknowledges TCAG/DGV. doi: 10.1007/s00702-019-02114-09. PubMed PMID: 31838600

Rare copy number variants in individuals at clinical high risk for psychosis: enrichment of synaptic/brain-related functional pathways
Jagannath V, Grünblatt E, Theodoridou A, Oneda B, Roth A, Gerstenberg M, Franscini M, Traber-Walker N, Correll CU, Heekeren K, Rössler W, Rauch A, Walitza S. Am J Med Genet B Neuropsychiatr Genet. 2020 Mar;183(2):140-151. Acknowledges TCAG/DGV. doi: 10.1002/ajmg.b.32770. PubMed PMID: 31742845

Copy number variation-based gene set analysis reveals cytokine signalling pathways associated with psychiatric comorbidity in patients with inflammatory bowel disease
Frenkel S, Bernstein CN, Sargent M, Jiang W, Kuang Q, Xu W, Hu P (2020). 2020 Jan;112(1):683-693. Acknowledges Bhooma Thiruvahindrapuram, John Wei. doi: 10.1016/j.ygeno.2019.05.001. Epub 2019 May 7. PubMed PMID: 31075388

Quantification of mRNA ribosomal engagement in human neurons using parallel translating ribosome affinity purification (TRAP) and RNA sequencing
Rodrigues DC, Mufteev M, Ellis J. STAR Protoc. 2020 Dec 18;2(1):100229. Acknowledges TCAG. doi: 10.1016/j.xpro.2020.100229. eCollection 2021 Mar 19. PubMed PMID: 33364619. PubMed Central PMCID: PMC7753199

Genomic footprints of an old affair: single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions
Tonzo V, Papadopoulou A, Ortego J. Mol Ecol. 2020 Jun;29(12):2254-2268. Illumina sequencing; also acknowledges Sergio Pereira. doi: 10.1111/mec.15475. Epub 2020 Jun 3. PubMed PMID: 32418257

Incorporating interspecific interactions into phylogeographic models: A case study with Californian oaks
Ortego J, Knowles LL. Mol Ecol. 2020. Dec;29(23):4510-4524. Illumina sequencing; also acknowledges Sergio Pereira. doi: 10.1111/mec.15548 Epub 2020 Jul 31. PubMed PMID: 32657460

Exome and genome sequencing in adults with undiagnosed disease: a prospective cohort study
Shickh S, Gutierrez Salazar M, Zakoor KR, Lázaro C, Gu J, Goltz J, Kleinman D, Noor A, Khalouei S, Mighton C, Reble E, Kodida R, Bombard Y, DiTroia S, Baxter S, Watkins N, Care M, Adler A, Horsburgh S, Morar O, Murphy J, Nevay DL, Szybowska M, Aronson M, Panchal S, Godoy R, Holter S, Randall Armel S, Semotiuk K, Elser C, Kim RH, Chitayat D, So J, Faghfoury H, Silver J, Morel CF, Lerner-Ellis J. J Med Genet. 2020 Jun 24:jmedgenet-2020-106936. WGS; also acknowledges TCAG in general. doi: 10.1136/jmedgenet-2020-106936. Epub 2020 Jun 24. PubMed PMID: 32581083

Connectivity mapping of a chronic kidney disease progression signature identified lysine deacetylases as novel therapeutic targets
Williams VR, Konvalinka A, Song X, Zhou X, John R, Pei Y, Scholey JW. Kidney Int. 2020 Jul;98(1):116-132. TCAG technical assistance. doi: 10.1016/j.kint.2020.01.029. Epub 2020 Feb 19. PubMed PMID: 32418621

Digital microfluidic isolation of single cells for -Omics
Lamanna J, Scott EY, Edwards HS, Chamberlain MD, Dryden MDM, Peng J, Mair B, Lee A, Chan C, Sklavounos AA, Heffernan A, Abbas F, Lam C, Olson ME, Moffat J, Wheeler AR. Nat Commun. 2020 Nov 11;11(1):5632. STR genotyping, Sanger sequencing. doi: 10.1038/s41467-020-19394-5. PubMed PMID: 33177493. PubMed Central PMCID: PMC7658233

Characterization of mutational status, spheroid formation, and drug response of a new genomically-stable human ovarian clear cell carcinoma cell line, 105C
Kolendowski B, Valdes YR, Hirte H, Itamochi H, Lee W, Carey M, Shepherd TG, DiMattia GE. Cells. 2020 Nov 3;9(11):2408. STR genotyping, Affymetrix CytoScan HD arrays. doi: 10.3390/cells9112408. PubMed PMID: 33153119. PubMed Central PMCID: PMC7693681

Gene fusions characterize a subset of uterine cellular leiomyomas
Hodgson A, Swanson D, Tang S, Dickson BC, Turashvili G. Genes Chromosomes Cancer. 2020 Jul 17. doi: 10.1002/gcc.22888. Sanger sequencing; also acknowledges Guillermo Casallo and Tara Paton. PubMed PMID: 32677742

Everolimus rescues the phenotype of elastin insufficiency in patient induced pluripotent stem cell-derived vascular smooth muscle cells
Kinnear C, Agrawal R, Loo C, Pahnke A, Rodrigues DC, Thompson T, Akinrinade O, Ahadian S, Keeley F, Radisic M, Mital S, Ellis J. Arterioscler Thromb Vasc Biol. 2020 May;40(5):1325-1339. Karyotyping, Sanger sequencing, NGS, and TCAG in general. doi: 10.1161/ATVBAHA.119.313936. Epub 2020 Mar 26. PubMed PMID: 32212852. PubMed Central PMCID: PMC7176340

COG5 variants lead to complex early onset retinal degeneration, upregulation of PERK and DNA damage
Tabbarah S, Tavares E, Charish J, Vincent A, Paterson A, Di Scipio M, Yin Y, Mendoza-Londono R, Maynes J, Heon E, Monnier PP. Sci Rep. 2020 Dec 4;10(1):21269. Illumina arrays, Illumina sequencing. doi: 10.1038/s41598-020-77394-3 PubMed PMID: 33277529 PubMed Central PMCID: PMC7718911

Effect of polymeric support material on biofilm development, bacterial population, and wastewater treatment performance in anaerobic fixed-film systems
Zhou Y, Kiely PD, Kibbee R, Ormeci B. Chemosphere. 2021 Feb;264(Pt 1):128477. doi: 10.1016/j.chemosphere.2020.128477. Epub 2020 Sep 30 PubMed. PMID: 33032216

Two distinct Dehalobacter strains sequentially dechlorinate 1,1,1-trichloroethane and 1,1-dichloroethane at a field site treated with granular zero valent iron and guar gum
Yang MI, Previdsa M, Edwards EA, Sleep BE. Water Res. 2020 Nov 1;186:116310. doi: 10.1016/j.watres.2020.116310. Epub 2020 Aug 17. PubMed PMID: 32858243

BRAF V600E mutation and MET amplification as resistance pathways of the second-generation anaplastic lymphoma kinase (ALK) inhibitor Alectinib in lung cancer
Shi R, Filho SNM, Li M, Fares A, Weiss J, Pham NA, Ludkovski O, Raghavan V, Li Q, Ravi D, Cabanero M, Moghal N, Leighl NB, Bradbury P, Sacher A, Shepherd FA, Yasufuku K, Tsao MS, Liu G. Lung Cancer. 2020 Aug;146:78-85. doi: 10.1016/j.lungcan.2020.05.018. Epub 2020 May 21. PubMed PMID: 32521388

Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21
Hussain A, Voisin V, Poon S, Karamboulas C, Bui NHB, Meens J, Dmytryshyn J, Ho VW, Tang KH, Paterson J, Clarke BA, Bernardini MQ, Bader GD, Neel BG, Ailles LE. J Exp Med. 2020 Aug 3;217(8):e20191094. doi: 10.1084/jem.20191094. PubMed PMID: 32434219. PubMed Central PMCID: PMC7398174


Sequencing

Using genomic tools to inform management of the Atlantic northern fulmar
Colston-Nepali L, Provencher JF, Mallory ML, Franckowiak RP, Sun Z, Robertson GL, Friesen VL. Conservation Genetics 2020, 21:1037-1050. doi: 10.1007/s10592-020-01309-y

Adipose tissue inflammation is directly linked to obesity-induced insulin resistance, while gut dysbiosis and mitochondrial dysfunction are not required
Petrick HL, Foley KP, Zlitni S, Brunetta HS, Paglialunga S, Miotto PM, Politis-Barber V, O'Dwyer C, Philbrick DJ, Fullerton MD, Schertzer JD, Holloway GP. Function 2020, 1(2):zqaa013. Mouse WGS. doi: 10.1093/function.zqaa013

Novel heterozygous PIK3CD mutation presenting with only laboratory markers of combined immunodeficiency
Mandola AB, Dadi H, Reid B, Roifman CM. Lymphosign J 2020, 7(2). Exome sequencing. doi: 10.14785/lymphosign-2020-0003

Paraphyletic species no more - genomic data resolve a Pleistocene radiation and validate morphological species of the Melanoplus scudderi complex (Insecta: Orthoptera)
Huang J-P, Hill JG, Orteo J, Knowles LL. Systematic Entomology 2020, 45(3):594-605. Illumina. doi.org/10.1111/syen.12415

Phylogenomics identifies a new major subgroup of apicomplexans, Marosporida class. nov., with extreme apicoplast genome reduction
Mathur V, Kwong WK, Husnik F, Irwin NAT, Kristmundsson A, Gestal C, Freeman M, Keeling PJ. Genome Biol Evol 2020, evaa244. WGS. doi: 10.1093/gbe/evaa244. PubMed PMID: 33566096. PubMed Central PMCID: PMC7875001

Genomic insights into the origin of trans-Mediterranean disjunct distributions
Noguerales V, Cordero PJ, Knowles LL, Ortego J. J Biogeography 27 November 2020 doi: 10.1111/jbi.14011. Illumina

Safeguarding the genetic integrity of native pollinators requires stronger regulations on commercial lines
Bartomeus I, Molina FP, Hidalgo-Galiana A, Ortego J. Ecol Solutions and Evidence 2020, 1(1):e12012. Illumina. doi: 10.1002/2688-8319.12012

Dispersal barriers and opportunities drive multiple levels of phylogeographic concordance in the Southern Alps of New Zealand
Marske KA, Thomaz AT, Knowles LL. Mol Ecol. 2020 Dec;29(23):4665-4679. Illumina. doi: 10.1111/mec.15655. Epub 2020 Oct 24. PubMed PMID: 32991032

Common barriers, but temporal dissonance: Genomic tests suggest ecological and paleo-landscape sieves structure a coastal riverine fish community
Thomaz AT, Knowles LL. Mol Ecol. 2020 Feb;29(4):783-796. Illumina. doi: 10.1111/mec.15357. Epub 2020 Feb 11. PubMed PMID: 31958183

Increased mitochondrial and lipid metabolism is a conserved effect of Insulin/PI3K pathway downregulation in adipose tissue
Bettedi L, Yan A, Schuster E, Alic N, Foukas LC. Sci Rep. 2020 Feb 25;10(1):3418. RNA-seq. doi: 10.1038/s41598-020-60210-3. PubMed PMID: 32099025. PubMed Central PMCID: PMC7042323

DNA polymerase and mismatch repair exert distinct microsatellite instability signatures in normal and malignant human cells
Chung J, Maruvka YE, Sudhaman S, Kelly J, Haradhvala NJ, Bianchi V, Edwards M, Forster VJ, Nunes NM, Galati MA, Komosa M, Deshmukh S, Cabric V, Davidson S, Zatzman M, Light N, Hayes R, Brunga L, Anderson ND, Ho B, Hodel KP, Siddaway R, Morrissy AS, Bowers DC, Larouche V, Bronsema A, Osborn M, Cole KA, Opocher E, Mason G, Thomas GA, George B, Ziegler DS, Lindhorst S, Vanan M, Yalon-Oren M, Reddy AT, Massimino M, Tomboc P, Van Damme A, Lossos A, Durno C, Aronson M, Morgenstern DA, Bouffet E, Huang A, Taylor MD, Villani A, Malkin D, Hawkins CE, Pursell ZF, Shlien A, Kunkel TA, Getz G, Tabori U. Cancer Discov. 2020 Dec 18:CD-20-0790. WGS. doi: 10.1158/2159-8290.CD-20-0790. PubMed PMID: 33355208

Testing which axes of species differentiation underlie covariance of phylogeographic similarity among montane sedge species
Hodel RGJ, Massatti R, Bishop SGD, Knowles LL. Evolution. 2021 Jan 2. doi: 10.1111/evo.14159. Illumina. Epub 2021 Jan 12. PubMed PMID: 33386752

Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust (Dociostaurus maroccanus)
González-Serna MJ, Cordero PJ, Ortego J. Ecol Evol. 2020 Mar 31;10(9):3991-4008. Illumina. doi: 10.1002/ece3.6165. eCollection 2020 May. PubMed PMID: 32489626. PubMed Central PMCID: PMC7244894

Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model
Nyangahu DD, Darby M, Havyarimana E, Brown BP, Horsnell W, Jaspan HB. Parasite Immunol. 2020 Sep;42(9):e12721. Illumina. doi: 10.1111/pim.12721. Epub 2020 May 3. PubMed PMID: 32277499. PubMed Central PMCID: PMC7423732

Comprehensive profiling of an aging immune system reveals clonal GZMK+ CD8+ T cells as conserved hallmark of inflammaging
Mogilenko DA, Shpynov O, Andhey PS, Arthur L, Swain A, Esaulova E, Brioschi S, Shchukina I, Kerndl M, Bambouskova M, Yao Z, Laha A, Zaitsev K, Burdess S, Gillfilan S, Stewart SA, Colonna M, Artyomov MN. Immunity. 2021 Jan 12;54(1):99-115.e12. RNA-seq. doi: 10.1016/j.immuni.2020.11.005. Epub 2020 Dec 2. PubMed PMID: 33271118

BORIS/CTCFL promotes a switch from a proliferative towards an invasive phenotype in melanoma cells
Janssen SM, Moscona R, Elchebly M, Papadakis AI, Redpath M, Wang H, Rubin E, van Kempen LC, Spatz A. Cell Death Discov. 2020 Jan 2;6(1):1. RNA-seq. doi: 10.1038/s41420-019-0235-x. eCollection 2020. PubMed PMID: 32123577. PubMed Central PMCID: PMC7026120

[6S]-5-methyltetrahydrofolic acid and folic acid pregnancy diets differentially program metabolic phenotype and hypothalamic gene expression of wistar rat dams post-birth
Pannia E, Hammoud R, Simonian R, Arning E, Ashcraft P, Wasek B, Bottiglieri T, Pausova Z, Kubant R, Anderson GH. Nutrients. 2020 Dec 25;13(1):48. RNA-seq. doi: 10.3390/nu13010048. PubMed PMID: 33375730. PubMed Central PMCID: PMC7823556

A frog with three sex chromosomes that co-mingle together in nature: Xenopus tropicalis has a degenerate W and a Y that evolved from a Z chromosome
Furman BLS, Cauret CMS, Knytl M, Song XY, Premachandra T, Ofori-Boateng C, Jordan DC, Horb ME, Evans BJ. PLoS Genet. 2020 Nov 9;16(11):e1009121. RNA-seq. doi: 10.1371/journal/pgen.1009121. PubMed PMID: 33166278. PubMed Central PMCID: PMC7652241

RNA expression profiling reveals PRAME, a potential immunotherapy target, is frequently expressed in solitary fibrous tumors
Wang WL, Gokgoz N, Samman B, Andrulis IL, Wunder JS, Demicco EG. Mod Pathol. 2020 Oct 2. doi: 10.1038/s41379-020-00687-5. RNA-seq. doi: 10.1038/s41379-020-00687-05. PubMed PMID: 33009490

A 38-gene model comprised of key TET2-associated genes shows additive utility to high-risk prostate cancer cases in the prognostication of biochemical recurrence
Kamdar S, Fleshner NE, Bapat B. BMC Cancer. 2020 Oct 2;20(1):953. RNA-seq. doi: 10.1186/s12885-020-07439-4. PubMed PMID: 33008340. PubMed Central PMCID: PMC7530956

Hippocampal DNA methylation in a mouse model of fetal alcohol spectrum disorder that includes maternal separation stress only partially explains changes in gene expression
Alberry BLJ, Singh SM. Front Genet. 2020 Feb 27;11:70. RNA-seq. doi: 10.3389/fgene.2020.00070. eCollection 2020. PubMed PMID: 32174962. PubMed Central PMCID: PMC7056727

Effect of long-acting β-agonists/glucocorticoids on human airway epithelial cell cytokine, transcriptomic and oxidative stress responses to cannabis smoke
Huff RD, Aguiar JA, Tse W, Stämpfli MR, McConkey BJ, Doxey AC, Hirota JA. ERJ Open Res. 2020 Jan 20;6(1):00265-2019. RNA-seq. doi: 10.1183/23120541.00265-2019. eCollection 2020 Jan. PubMed PMID: 31984210. PubMed Central PMCID: PMC6970181

Thiomicrorhabdus streamers and sulfur cycling in perennial hypersaline cold springs in the Canadian high arctic
Magnuson E, Mykytczuk NCS, Pellerin A, Goordial J, Twine SM, Wing B, Foote SJ, Fulton K, Whyte LG. Environ Microbiol. 2020 Jan 13. doi: 10.1111/1462-2920.14916. Roche and Illumina. PubMed PMID: 31943734

Decimated little brown bats show potential for adaptive change
Auteri GG, Knowles LL. Sci Rep. 2020 Feb 20;10(1):3023. Illumina. doi: 10.1038/s41598-020-59797-4. PubMed PMID: 32080246. PubMed PMCID: PMC7033193

Phenotype driven analysis of whole genome sequencing identifies deep intronic variants that cause retinal dystrophies by aberrant exonization
Di Scipio M, Tavares E, Deshmukh S, Audo I, Green-Sanderson K, Zubak Y, Zine-Eddine F, Pearson A, Vig A, Tang CY, Mollica A, Karas J, Tumber A, Yu CW, Billingsley G, Wilson MD, Zeitz C, Héon E, Vincent A. Invest Ophthalmol Vis Sci. 2020 Aug 3;61(10):36. NGS. doi: 10.1167/iovs.61.10.36. PubMed PMID: 32881472. PubMed Central PMCID: PMC7443117

Molecular mechanism linking a novel PCSK9 copy number variant to severe hypercholesterolemia
Lau P, Soubeyrand S, Hegele RA, Lagace TA, McPherson R. Atherosclerosis. 2020 Jul;304:39-43. WGS. doi: 10.1016/j.atherosclerosis.2020.05.013. Epub 2020 May 28. PubMed PMID: 32585424

Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure
Heidemann S, Bursic B, Zandi S, Li H, Abelson S, Klaassen RJ, Abish S, Rayar M, Breakey VR, Moshiri H, Dhanraj S, de Borja R, Shlien A, Dick JE, Dror Y. JCI Insight. 2020 Feb 27;5(4):e131018. Illumina. doi: 10.1172/jci.insight.131018. PubMed PMID: 31990679. PubMed Central PMCID: PMC7101147

The role of introgression and ecotypic parallelism in delineating intraspecific conservation units
Taylor RS, Manseau M, Horn RL, Keobouasone S, Golding GB, Wilson PJ. Mol Ecol. 2020 Aug;29(15):2793-2809. Illumina. doi: 10.1111/mec.15522. Epub 2020 Jul 11. PubMed PMID: 32567754. PubMed Central PMCID: PMC7496186

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant
Spasov E, Tsuji JM, Hug LA, Doxey AC, Sauder LA, Parker WJ, Neufeld JD. ISME J. 2020 Jul;14(7):1857-1872. Illumina. doi: 10.1038/s41396-020-0650-2. Epub 2020 Apr 24. PubMed PMID: 32332864. PubMed Central PMCID: PMC7305129

Canadian polar bear population structure using genome-wide markers
Jensen EL, Tschritter C, de Groot PVC, Hayward KM, Branigan M, Dyck M, Clemente-Carvalho RBG, Lougheed SC. Ecol Evol. 2020 Mar 24;10(8):3706-3714. Illumina. doi: 10.1002/ece3.6159. eCollection 2020 Apr. PubMed PMID: 32313629. PubMed Central PMCID: PMC7160183

Hedgehog-activated Fat4 and PCP pathways mediate mesenchymal cell clustering and villus formation in gut development
Rao-Bhatia A, Zhu M, Yin WC, Coquenlorge S, Zhang X, Woo J, Sun Y, Dean CH, Liu A, Hui CC, Shivdasani RA, McNeill H, Hopyan S, Kim TH. Dev Cell. 2020 Mar 9;52(5):647-658.e6. Illumina. doi: 10.1016/j.devcel.2020.02.003. PubMed PMID: 32155439

Genetic diversity of strawberry mild yellow edge virus from eastern Canada
Xiang Y, Nie X, Bernardy M, Liu JJ, Su L, Bhagwat B, Dickison V, Holmes J, Grose JM, Creelman AC. Arch Virol. 2020 Apr;165(4):923-935. Illumina. doi: 10.1007/s00705-020-04561-2. PubMed PMID: 32128611

Bovine lactoferrin supplementation does not disrupt microbiota development in preterm infants receiving probiotics
Grzywacz K, Butcher J, Li J, Barrington K, Mohamed I, Stintzi A. J Pediatr Gastroenterol Nutr. 2020 Aug;71(2):216-222. Illumina rRNA amplicon sequencing. doi: 10.1097/MPG.0000000000002734. PubMed PMID: 32404742

MicroRNA profile of patients with chronic limb-threatening ischemia
Syed MH, Zamzam A, Valencia J, Khan H, Jain S, Singh KK, Abdin R, Qadura M. Diagnostics (Basel). 2020 Apr 17;10(4):230. Illumina microRNA sequencing. doi: 10.3390/diagnostics10040230. PubMed PMID: 32316437. PubMed Central PMCID: PMC7235988

A novel mouse model of Duchenne muscular dystrophy carrying a multi-exonic Dmd deletion exhibits progressive muscular dystrophy and early-onset cardiomyopathy
Wong TWY, Ahmed A, Yang G, Maino E, Steiman S, Hyatt E, Chan P, Lindsay K, Wong N, Golebiowski D, Schneider J, Delgado-Olguín P, Ivakine EA, Cohn RD. Dis Model Mech. 2020 Sep 21;13(9):dmm045369. Illumina WGS. doi: 10.1242/dmm.045369. PubMed PMID: 32988972. PubMed Central PMCID: PMC7522028

Quality of whole genome sequencing from blood versus saliva derived DNA in cardiac patients
Yao RA, Akinrinade O, Chaix M, Mital S. BMC Med Genomics. 2020 Jan 29;13(1):11. WGS. doi: 10.1186/s12920-020-0664-7. PubMed PMID: 31996208. PubMed Central PMCID: PMC6988365


Sanger Sequencing

Phylogeny and biogeography of the Brazilian-Guiana Shield endemic Corymbophanes clade of armoured catfishes (Loricariidae)
Lujan NK, Armbruster JW, Werkeke DC, Teixeira TF, Lovejoy NR. Zoological Journal of the Linnean Society, 2020, 188, 1213-1235. doi: 10.1093/zoolinnean/zlz090

Saccharomyces uvarum yeast isolate consumes acetic acid during fermentation of high sugar juice and juice with high starting volatile acidity
Kelly J, van Dyk SA, Dowling LK, Pickering GJ, Kemp B, Inglis DL. OENO One 2020, 54(1):199-211. doi: 10.20870/oeno-one.2020.54.2.2594

Reconstructing plastome evolution across the phylogenetic backbone of the parasitic plant genus Cuscuta (Convolvulaceae)
Banerjee A, Stefanovic S. Botanical Journal of the Linnean Society, 2020, 194, 423-438. doi: 10.1093/botlinnean/boaa056

Searching for bacteria in sticky situations: Methods for investigating bacterial survival at solid-air interfaces involving Wyoming MX-80 bentonite
Pashang R, Laursen AE. Applied Clay Science 2020, 188:105487. doi: 10.1016/j.clay.2020.105487

Dynamic changes in community composition of Scenedesmus-seeded artificial, engineered microalgal biofilms
Paquette AJ, Sharp CE, Schnurr PJ, Allen DG, Short SM, Espie GS. Algal Res 2020, 46:101805. doi: 10.1016/j.algal.2020.101805

Specific quantification of Scenedesmus obliquus and Chlorella vulgaris in mixed-species algal biofilms
Cheung SL, Allen DG, Short SM. Bioresource Tech 2020, 295:122251. doi: 10.1016/j.biortech.2019.122251

High production of cellulase by a newly isolated strain Paenibacillus sp. IM7
Almuharef I, Rahman MS, Qin W. Waste and Biomass Valorization 2020, 11:6085-6094. doi: 10.1007/s12649-019-00832-5

Selective neuronal degeneration in MATR3 S85C knock-in mouse model of early-stage ALS
Kao CS, van Bruggen R, Kim JR, Chen XXL, Chan C, Lee J, Cho WI, Zhao M, Arndt C, Maksimovic K, Khan M, Tan Q, Wilson MD, Park J. Nat Commun. 2020 Oct 20;11(1):5304. doi: 10.1038/s41467-020-18949-w

Molecular basis of bile- salt- and iron-induced enterohaemorrhagic E. coli resistance to cationicantimicrobial peptides
Kunwar CB, Birstonas S, McPhee JB, Barnett Foster D. Microbiology (Reading). 2020 Dec;166(12):1149-1159. doi: 10.1099/mic.0.000988. PubMed PMID: 33205745

Functional cross-talk of mbth-like proteins during thaxtomin biosynthesis in the potato common scab pathogen Streptomyces scabiei
Li Y, Tahlan K, Bignell DRD. Front Microbiol. 2020 Oct 15;11:585456 .doi: 10.3389/fmicb.2020.585456. PubMed PMID: 33178168. PubMed Central PMCID: PMC7593251

Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding
Qu C, Stewart KA, Clemente-Carvalho R, Zheng J, Wang Y, Gong C, Ma L, Zhao J, Lougheed SC. Sci Rep. 2020 Oct 7;10(1):16715. doi: 10.1038/s41598-020-73648-2. PubMed PMID: 33028872. PubMed Central PMCID: PMC7542144

Induced pluripotent stem cell line UOMi002-A from a patient with Leigh syndrome with compound heterozygous mutations in the NDUFV1 gene
Sequiera GL, Rockman-Greenberg C, Dhingra S. Stem Cell Res. 2020 Oct;48:101964. doi: 10.1016/j.scr.2020.101964. PubMed PMID: 32871395

Establishment of variant free-iPSC (UOMi003-A) line from patient with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes
Sequiera GL, Rockman-Greenberg C, Dhingra S. Stem Cell Res. 2020 Oct;48:101935. doi: 10.1016/j.scr.2020.101935. PubMed PMID: 32777772

Generation of human induced pluripotent stem cell (hiPSC) line UOMi001-A from a patient with Leigh-like syndrome harbouring compound heterozygous variants in ECHS1 gene
Sequiera GL, Rockman-Greenberg C, Dhingra S. Stem Cell Res. 2020 Oct;48:101934. doi: 10.1016/j.scr.2020.101934. PubMed PMID: 32777769

A comprehensive, flexible collection of SARS-CoV-2 coding regions
Kim DK, Knapp JJ, Kuang D, Chawla A, Cassonnet P, Lee H, Sheykhkarimli D, Samavarchi-Tehrani P, Abdouni H, Rayhan A, Li R, Pogoutse O, Coyaud É, van der Werf S, Demeret C, Gingras AC, Taipale M, Raught B, Jacob Y, Roth FP. G3 (Bethesda). 2020 Sep 2;10(9):3399-3402. doi: 10.1534/g3.120.401554. PubMed PMID: 32763951. PubMed Central PMCID: PMC7467003

Molecular phylogeny of sturgeon mimiviruses and Bayesian hierarchical modeling of their effect on wild Lake Sturgeon (Acipenser fulvescens) in Central Canada
Clouthier S, Caskenette A, Van Walleghem E, Schroeder T, Macdonald D, Anderson ED. Infect Genet Evol. 2020 Oct;84:104491. doi: 10.1016.j.meegid.2020.104491. PubMed PMID: 32763443

MRIP regulates the myosin IIA activity and DDR1 function to enable collagen tractional remodeling
Coelho NM, Wang A, Petrovic P, Wang Y, Lee W, McCulloch CA. Cells. 2020 Jul 11;9(7):1672. doi: 10.3390/cells9071672. PubMed PMID: 32664526. PubMed Central PMCID: PMC7407560

Adding insult to injury: mechanistic basis for how AmpC mutations allow Pseudomonas aeruginosa to accelerate cephalosporin hydrolysis and evade Avibactam
Slater CL, Winogrodzki J, Fraile-Ribot PA, Oliver A, Khajehpour M, Mark BL. Antimicrob Agents Chemother. 2020 Aug 20;64(9):e00894-20.

CAMKK2-CAMK4 signaling regulates transferrin trafficking, turnover, and iron homeostasis
Sabbir MG. Cell Commun Signal. 2020 May 27;18(1):80. doi: 10.1128/AAC.00894-20. PubMed PMID: 32660987. PubMed Central PMCID: PMC7449160

SCO-spondin defects and neuroinflammation are conserved mechanisms driving spinal deformity across genetic models of idiopathic scoliosis
Rose CD, Pompili D, Henke K, Van Gennip JLM, Meyer-Miner A, Rana R, Gobron S, Harris MP, Nitz M, Ciruna B. Curr Biol. 2020 Jun 22;30(12):2363-2373.e6.

Low phosphatase activity of LiaS and strong LiaR-DNA affinity explain the unusual LiaS to LiaR in vivo stoichiometry
Jani S, Sterzenbach K, Adatrao V, Tajbakhsh G, Mascher T, Golemi-Kotra D. BMC Microbiol. 2020 Apr 29;20(1):104. doi: 10.1016/j.cub.2020.04.020. PubMed PMID: 32386528

Expression profiling, downstream signaling, and inter- subunit interactions of GPA2/GPB5 in the adult mosquito Aedes aegypti
Rocco DA, Paluzzi JV. Front Endocrinol (Lausanne). 2020 Mar 31;11:158. doi: 10.3389/fendo.2020.00158. PubMed PMID: 32296389. PubMed Central PMCID: PMC7137729

Sorafenib as an Inhibitor of RUVBL2
Nano N, Ugwu F, Seraphim TV, Li T, Azer G, Isaac M, Prakesch M, Barbosa LRS, Ramos CHI, Datti A, Houry WA. Biomolecules. 2020 Apr 14;10(4):605. doi: 10.3390/biom10040605. PubMed PMID: 32295120. PubMed Central PMCID: PMC7226205

Integrated strain engineering and bioprocessing strategies for high-level bio-based production of 3-hydroxyvalerate in Escherichia coli
Miscevic D, Mao JY, Kefale T, Abedi D, Huang CC, Moo-Young M, Chou CP. Appl Microbiol Biotechnol. 2020 Jun;104(12):5259-5272. doi: 10.1007/s00253-020-10580-5. PubMed PMID: 32291486

Influence of dietary iron exposure on trace metal homeostasis and expression of metal transporters during development in zebrafish
Chandrapalan T, Kwong RWM. Environ Pollut. 2020 Jun;261:114159. doi: 10.1016/j.envpol.2020.114159. PubMed PMID: 32113105

Mfsd8 localizes to endocytic compartments and influences the secretion of Cln5 and cathepsin D in Dictyostelium
Huber RJ, Mathavarajah S, Yap SQ. Cell Signal. 2020 Jun;70:109572. doi: 10.1016/j.cellsig.2020.109572. PubMed PMID: 32087303

Bacterial exposure mediates developmental plasticity and resistance to lethal Vibrio lentus infection in purple sea urchin (Strongylocentrotus purpuratus) larvae
Schuh NW, Carrier TJ, Schrankel CS, Reitzel AM, Heyland A, Rast JP. Front Immunol. 2020 Jan 14;10:3014. doi: 10.3389/fimmu.2019.03014. PubMed PMID: 31993052. PubMed Central PMCID: PMC6971090

A reference library for assigning protein subcellular localizations by image-based machine learning
Schormann W, Hariharan S, Andrews DW. J Cell Biol. 2020 Mar 2;219(3):e201904090. doi: 10.1083/jcb.201904090. PubMed PMID: 31968357. PubMed Central PMCID: PMC7055006

High-level heterologous production of propionate in engineered Escherichia coli
Miscevic D, Mao JY, Moo-Young M, Chou CP. Biotechnol Bioeng. 2020 May;117(5):1304-1315. doi: 10.1002/bit.27276. PubMed PMID: 31956980

Exome sequencing identifies de novo splicing variant in XRCC6 in sporadic case of autism
Sjaarda CP, Wood S, McNaughton AJM, Taylor S, Hudson ML, Liu X, Guerin A, Ayub M. J Hum Genet. 2020 Mar;65(3):287-296. doi: 10.1038/s10038-019-0707-0. PubMed PMID: 31827253

Heterologous production of 3-hydroxyvalerate in engineered Escherichia coli
Miscevic D, Srirangan K, Kefale T, Kilpatrick S, Chung DA, Moo-Young M, Chou CP. Metab Eng. 2020 Sep;61:141-151. doi: 10.1016/j.ymben.2019.11.005. PubMed PMID: 31726215

BraInMap elucidates the macromolecular connectivity landscape of mammalian brain
Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. Cell Syst. 2020 Apr 22;10(4):333-350.e14. doi: 10.1016/j.cels.2020.03.003. PubMed PMID: 32325033. PubMed PMCID: PMC7938770


Genetics Analysis

Single nucleotide polymorphisms in sweet, fat, umami, salt, bitter and sour taste receptor genes are associated with gustatory function and taste preferences in young adults
Chamoun E, Liu AS, Duizer LM, Feng Z, Darlington G, Duncan AM, Haines J, Ma DWL. Nutrition Res, 05 December 2020. Agena genotyping. doi: 10.1016/j.nutres.2020.12.007. PubMed PMID: 33444969

MRI- guided focused ultrasound enhances drug delivery in experimental diffuse intrinsic pontine glioma
Ishida J, Alli S, Bondoc A, Golbourn B, Sabha N, Mikloska K, Krumholtz S, Srikanthan D, Fujita N, Luck A, Maslink C, Smith C, Hynynen K, Rutka J. J Control Release. 2020 Nov 11:S0168-3659(20)30659-3. STR genotyping. doi: 10.1016/j.jconrel.2020.11.010. PubMed PMID: 33188825

Berthiaume LG. Targeting N-myristoylation for therapy of B-cell lymphomas
Beauchamp E, Yap MC, Iyer A, Perinpanayagam MA, Gamma JM, Vincent KM, Lakshmanan M, Raju A, Tergaonkar V, Tan SY, Lim ST, Dong WF, Postovit LM, Read KD, Gray DW, Wyatt PG, Mackey JR, Berthiaume LG. Nat Commun. 2020 Oct 22;11(1):5348. STR genotyping. doi: 10.1038/s41467-020-18998-1. PubMed PMID: 33093447. PubMed Central PMCID: PMC7582192

Material properties of disulfide-crosslinked hyaluronic acid hydrogels influence prostate cancer cell growth and metabolism
Tam NW, Chung D, Baldwin SJ, Simmons JR, Xu L, Rainey JK, Dellaire G, Frampton JP. J Mater Chem B. 2020 Nov 4;8(42):9718-9733. STR genotyping. doi: 10.1039/d0tb01570a. PubMed PMID: 33015692

Adipose tissue from lean and obese mice induces a mesenchymal to epithelial transition-like effect in triple negative breast cancers cells grown in 3-dimensional culture
Asante EC, Pallegar NK, Hoffmann AJ, Viloria-Petit AM, Christian SL. Int J Mol Sci. 2020 Sep 3;21(17):6439. STR genotyping. doi: 10.3390/ijms21176439. PubMed PMID: 32899433. PubMed Central PMCID: PMC7503907

Recognition of semaphorin proteins by P. sordellii lethal toxin reveals principles of receptor specificity in clostridial toxins
Lee H, Beilhartz GL, Kucharska I, Raman S, Cui H, Lam MHY, Liang H, Rubinstein JL, Schramek D, Julien JP, Melnyk RA, Taipale M. Cell. 2020 Jul 23;182(2):345-356.e16. STR genotyping. doi: 10.1016/j.cell.2020.06.005. PubMed PMID: 32589945. PubMed Central PMCID: PMC7316060

Functional genomics identifies new synergistic therapies for retinoblastoma
Aubry A, Pearson JD, Huang K, Livne-Bar I, Ahmad M, Jagadeesan M, Khetan V, Ketela T, Brown KR, Yu T, Lu S, Wrana JL, Moffat J, Bremner R. Oncogene. 2020 Jul;39(31):5338-5357. STR genotyping. doi: 10.1038/s41388-020-1372-7. PubMed PMID: 32572160. PubMed Central PMCID: PMC7391301

Mutant ACVR1 arrests glial cell differentiation to drive tumorigenesis in pediatric gliomas
Fortin J, Tian R, Zarrabi I, Hill G, Williams E, Sanchez-Duffhues G, Thorikay M, Ramachandran P, Siddaway R, Wong JF, Wu A, Apuzzo LN, Haight J, You-Ten A, Snow BE, Wakeham A, Goldhamer DJ, Schramek D, Bullock AN, Dijke PT, Hawkins C, Mak TW. Cancer Cell. 2020 Mar 16;37(3):308-323.e12. STR genotyping. doi: 10.1016/j.ccell.2020.02.002. PubMed PMID: 32142668. PubMed Central PMCID: PMC7105820

The carboxyl-terminal sequence of bim enables bax activation and killing of unprimed cells
Chi X, Nguyen D, Pemberton JM, Osterlund EJ, Liu Q, Brahmbhatt H, Zhang Z, Lin J, Leber B, Andrews DW. Elife. 2020 Jan 24;9:e44525. STR genotyping. doi: 10.7554/eLife.44525. PubMed PMID: 31976859. PubMed Central PMCID: PMC6980855

Comprehensive analysis of 204 sporadic hydatidiform moles: revisiting risk factors and their correlations with the molar genotypes
Khawajkie Y, Mechtouf N, Nguyen NMP, Rahimi K, Breguet M, Arseneau J, Ronnett BM, Hoffner L, Lazure F, Arnaud M, Peers F, Tan L, Rafea BA, Aguinaga M, Horowitz NS, Ao A, Tan SL, Brown R, Buckett W, Surti U, Hovanes K, Sahoo T, Sauthier P, Slim R. Mod Pathol. 2020 May;33(5):880-892. STR genotyping. doi: 10.1038/s41379-019-0432-4. PubMed PMID: 31857680

Sleep Fragmentation and Cognitive Trajectories After Critical Illness
Wilcox ME, McAndrews MP, Van J, Jackson JC, Pinto R, Black SE, Lim AS, Friedrich JO, Rubenfeld GD. Chest. 2021 Jan;159(1):366-381. SNaPshot genotyping. doi: 10.1016/j.chest.2020.07.036. PubMed PMID: 32717265

Ultrasensitive and rapid quantification of rare tumorigenic stem cells in hPSC-derived cardiomyocyte populations
Wang Z, Gagliardi M, Mohamadi RM, Ahmed SU, Labib M, Zhang L, Popescu S, Zhou Y, Sargent EH, Keller GM, Kelley SO. Sci Adv. 2020 Mar 20;6(12):eaay7629. ddPCR. doi: 10.1126/sciadv.aay7629. PubMed PMID: 32440533. PubMed Central PMCID: PMC7227422

Serotonin system genes and hoarding with and without other obsessive-compulsive traits in a population-based, pediatric sample: a genetic association study
Sinopoli VM, Erdman L, Burton CL, Park LS, Dupuis A, Shan J, Goodale T, Shaheen SM, Crosbie J, Schachar RJ, Arnold PD. Depress Anxiety. 2020 Aug;37(8):760-770. Genotyping. doi: 10.1002/da.22996. PubMed PMID: 32092211

T cell-intrinsic CX3CR1 marks the most differentiated effector CD4+ T Cells, but is largely dispensable for CD4+ T cell responses during chronic viral infection
Batista NV, Chang YH, Chu KL, Wang KC, Girard M, Watts TH. Immunohorizons. 2020 Nov 10;4(11):701-712. Mouse SNP genotyping panel. Doi: 10.4049/immunohorizons.2000059. PubMed PMID: 33172841


Statistical Analysis

APOL1 risk variants and subclinical cardiovascular disease in incident hemodialysis patients
Chen TK, Fitzpatrick J, Winkler CA, Binns-Roemer EA, Corona-Villalobos CP, Jaar BG, Sozio SM, Parekh RS, Estrella M. Kidney International Reports, 20 Nov. 2020 doi: 10.1016/j.ekir.2020.11.006. PubMed PMID: 33615058. PubMed Central PMCID: PMC7879092


Biobanking

Mutant p53 induces Golgi tubulo-vesiculation driving a prometastatic secretome
Capaci V, Bascetta L, Fantuz M, Beznoussenko GV, Sommaggio R, Cancila V, Bisso A, Campaner E, Mironov AA, Wisniewski JR, Ulloa Severino L, Scaini D, Bossi F, Lees J, Alon N, Brunga L, Malkin D, Piazza S, Collavin L, Rosato A, Bicciato S, Tripodo C, Mantovani F, Del Sal G. Nat Commun. 2020 Aug 7;11(1):3945. Skin biopsy culture. doi: 10.1038/s41467-020-17596-5. PubMed PMID: 32770028. PubMed Central PMCID: PMC7414119

Early infantile epileptic encephalopathy due to biallelic pathogenic variants in PIGQ:Report of seven new subjects and review of the literature
Johnstone DL, Nguyen TTM, Zambonin J, Kernohan KD, St-Denis A, Baratang NV, Hartley T, Geraghty MT, Richer J, Majewski J, Bareke E, Guerin A, Pendziwiat M, Pena LDM, Braakman HMH, Gripp KW, Edmondson AC, He M, Spillmann RC, Eklund EA, Bayat A, McMillan HJ, Boycott KM, Campeau PM. J Inherit Metab Dis. 2020 Nov;43(6):1321-1332. Fibroblast culture. doi: 10.1002/jimd.12278. PubMed PMID: 32588908. PubMed PMCID: PMC7689772

Haploinsufficiency of RREB1 causes a Noonan-like RASopathy via epigenetic reprogramming of RAS-MAPK pathway genes
Kent OA, Saha M, Coyaud E, Burston HE, Law N, Dadson K, Chen S, Laurent EM, St-Germain J, Sun RX, Matsumoto Y, Cowen J, Montgomery-Song A, Brown KR, Ishak C, Rose J, De Carvalho DD, He HH, Raught B, Billia F, Kannu P, Rottapel R. Nat Commun. 2020 Sep 16;11(1):4673. EBV-transformed cell lines. doi: 10.1038/s41467-020-18483-9. PubMed PMID: 32938917. PubMed Central PMCID: PMC7495420


Genome Resources

A non-canonical Hedgehog pathway initiates ciliogenesis and autophagy
Akhshi T, Trimble WS.J Cell Biol. 2021 Jan 4;220(1):e202004179. BAC clone. doi: 10.1083/jcb.202004179. PubMed PMID: 33258871. PubMed Central PMCID: PMC7714386


Microarray

S100A10 has a critical regulatory function in mammary tumor growth and metastasis: insights using MMTV-PyMT oncomice and clinical patient sample analysis
Bharadwaj AG, Dahn ML, Liu RZ, Colp P, Thomas LN, Holloway RW, Marignani PA, Too CK, Barnes PJ, Godbout R, Marcato P, Waisman DM. Cancers (Basel). 2020 Dec 7;12(12):3673. Affymetrix expression arrays. doi: 10.3390/cancers12123673. PubMed PMID: 33297495. PubMed Central PMCID: PMC7762402

Molecular attributes underlying central nervous system and systemic relapse in diffuse large B-cell lymphoma
Isaev K, Ennishi D, Hilton L, Skinnider B, Mungall KL, Mungall AJ, Bakhtiari M, Tremblay-LeMay R, Silva A, Ben-Neriah S, Boyle M, Villa D, Marra MA, Steidl C, Gascoyne RD, Morin R, Savage KJ, Scott DW, Kridel R. Haematologica. 2020 Aug 13. doi: 10.3324/haematol.2020.255950. Affymetrix expression arrays. PubMed PMID: 32817292

Lung group 2 innate lymphoid cells are trained by endogenous IL-33 in the neonatal period.
Steer CA, Mathä L, Shim H, Takei F. JCI Insight. 2020 Jul 23;5(14):e135961. Affymetrix expression arrays. doi: 10.1172/jci.insight.135961. PubMed PMID: 32573494. PubMed Central PMCID: PMC7453888

The strategic combination of trastuzumab emtansine with oncolytic rhabdoviruses leads to therapeutic synergy
Arulanandam R, Taha Z, Garcia V, Selman M, Chen A, Varette O, Jirovec A, Sutherland K, Macdonald E, Tzelepis F, Birdi H, Alluqmani N, Landry A, Bergeron A, Vanderhyden B, Diallo JS. Commun Biol. 2020 May 22;3(1):254. Affymetrix expression arrays. doi: 10.1038/s42003-020-0972-7. PubMed PMID: 32444806. PubMed Central PMCID: PMC7244474

A novel role for NUAK1 in promoting ovarian cancer metastasis through regulation of fibronectin production in spheroids
Fritz JL, Collins O, Saxena P, Buensuceso A, Ramos Valdes Y, Francis KE, Brown KR, Larsen B, Colwill K, Gingras AC, Rottapel R, Shepherd TG. Cancers (Basel). 2020 May 15;12(5):1250. Affymetrix expression arrays. doi: 10.3390/cancers12051250. PubMed PMID: 32429240. PubMed Central PMCID: PMC7280971

Learning-induced mRNA alterations in olfactory bulb mitral cells in neonatal rats
Nartey MN, Peña-Castillo L, LeGrow M, Doré J, Bhattacharya S, Darby-King A, Carew SJ, Yuan Q, Harley CW, McLean JH. Learn Mem. 2020 Apr 15;27(5):209-221. Affymetrix expression arrays. doi: 10.1101/lm.051177.119. PubMed PMID: 32295841. PubMed Central PMCID: PMC7164515

Loss of lenalidomide-induced megakaryocytic differentiation leads to therapy resistance in del(5q) myelodysplastic syndrome
Martinez-Høyer S, Deng Y, Parker J, Jiang J, Mo A, Docking TR, Gharaee N, Li J, Umlandt P, Fuller M, Jädersten M, Kulasekararaj A, Malcovati L, List AF, Hellström-Lindberg E, Platzbecker U, Karsan A. Nat Cell Biol. 2020 May;22(5):526-533. Affymetrix expression arrays. doi: 10.1038/s41556-020-0497-9. PubMed PMID: 32251398

miR-191 promotes radiation resistance of prostate cancer through interaction with RXRA
Ray J, Haughey C, Hoey C, Jeon J, Murphy R, Dura-Perez L, McCabe N, Downes M, Jain S, Boutros PC, Mills IG, Liu SK. Cancer Lett. 2020 Mar 31;473:107-117. Affymetrix expression arrays. doi: 10.1016/j.canlet.2019.12.025. PubMed PMID: 31874245

ALDH1A3-regulated long non-coding RNA NRAD1 is a potential novel target for triple-negative breast tumors and cancer stem cells
Vdovic D, Huynh TT, Konda P, Dean C, Cruickshank BM, Sultan M, Coyle KM, Gujar S, Marcato P. Cell Death Differ. 2020 Jan;27(1):363-378. Affymetrix expression arrays. doi: 10.1038/s41418-019-0362-1. PubMed PMID: 31197235. PubMed Central PMCID: PMC7206030

Transgenerational epigenetic and transcriptomic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure in rat
Prokopec SD, Viluksela M, Miettinen HM, Boutros PC, Pohjanvirta R (2020). Arch Toxicol. 2020 May;94(5):1613-1624. Affymetrix expression arrays. doi: 10.1007/s00204-020-02730-5. PubMed PMID: 32277265

Treatment of neuroblastoma cells with inhibitors of protein disulfide isomerase upregulates NQO1 activity
Özcelik D. Chem Res Toxicol. 2020 Aug 17;33(8):2099-2107 doi: 10.1021/acs.chemrestox.0c00101. PubMed PMID: 32662633

Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade-specific epigenome and transcriptome landscapes
Gagliardi A, Porter VL, Zong Z, Bowlby R, Titmuss E, Namirembe C, Griner NB, Petrello H, Bowen J, Chan SK, Culibrk L, Darragh TM, Stoler MH, Wright TC, Gesuwan P, Dyer MA, Ma Y, Mungall KL, Jones SJM, Nakisige C, Novik K, Orem J, Origa M, Gastier-Foster JM, Yarchoan R, Casper C, Mills GB, Rader JS, Ojesina AI, Gerhard DS, Mungall AJ, Marra MA. Nat Genet. 2020 Aug;52(8):800-810. Illumina methylation arrays. doi: 10.1038/s41588-020-0673-7. PubMed PMID: 32747824. PubMed Central PMCID: PMC7498180

Obsessive-compulsive disorder and attention-deficit/hyperactivity disorder: distinct associations with DNA methylation and genetic variation
Goodman SJ, Burton CL, Butcher DT, Siu MT, Lemire M, Chater-Diehl E, Turinsky AL, Brudno M, Soreni N, Rosenberg D, Fitzgerald KD, Hanna GL, Anagnostou E, Arnold PD, Crosbie J, Schachar R, Weksberg R. J Neurodev Disord. 2020 Aug 16;12(1):23. Illumina methylation arrays. doi: 10.1186/s11689-020-09324-3. PubMed PMID: 32799817. PubMed Central PMCID: PMC7429807

Decitabine response in breast cancer requires efficient drug processing and is not limited by multidrug resistance
Dahn ML, Cruickshank BM, Jackson AJ, Dean C, Holloway RW, Hall SR, Coyle KM, Maillet H, Waisman DM, Goralski KB, Giacomantonio CA, Weaver ICG, Marcato P. Mol Cancer Ther. 2020 May;19(5):1110-1122. Illumina methylation, Affymetrix expression arrays. doi: 10.1158/1535-7163.MCT-19-0745. PubMed PMID: 32156786

The effect of polymorphisms in startle-related genes on anxiety symptom severity
Tomasi J, Zai CC, Zai G, Herbert D, King N, Freeman N, Kennedy JL, Tiwari AK. J Psychiatr Res. 2020 Jun;125:144-151. Illumina SNP genotyping arrays. doi: 10.1016/j.jpsychires.2020.03.019. PubMed PMID: 32289651

Immunohistochemical and nanoString-Based Subgrouping of Clinical Medulloblastoma Samples
D'Arcy CE, Nobre LF, Arnaldo A, Ramaswamy V, Taylor MD, Naz-Hazrati L, Hawkins CE. J Neuropathol Exp Neurol. 2020 Apr 1;79(4):437-447. Illumina methylation arrays. doi: 10.1093/jnen/nlaa005. PubMed PMID: 32053195

Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents
Tharmalingam S, Khurana S, Murray A, Lamothe J, Tai TC. Sci Rep. 2020 Oct 30;10(1):18755. Rat expression arrays. doi: 10.1038/s41598-020-75652-y. PubMed PMID: 33127986. PubMed Central PMCID: PMC7603342


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