Research

Research from the GREGoR Stanford Site

X-CAP improves pathogenicity prediction of stopgain variants
Ruchir Rastogi, Peter D Stenson, David N Cooper, Gill Bejerano. Genome Med. 2022 Jul 29;14(1):81. PMID: 35906703

Toward transcriptomics as a primary tool for rare disease investigation
Stephen B Montgomery, Jonathan A Bernstein, Matthew T Wheeler. Cold Spring Harb Mol Case Stud. 2022 Mar 24;8(2):a006198. PMID: 35217565

Research from the Stanford Team

Combining Clinical and Polygenic Risk Improves Stroke Prediction Among Individuals With Atrial Fibrillation
O'Sullivan JW, Shcherbina A, Justesen JM, Turakhia M, Perez M, Wand H, Tcheandjieu C, Clarke SL, Rivas MA, Ashley EA. Circ Genom Precis Med. 2021 Jun;14(3):e003168. PMID: 34029116

A genome-wide atlas of co-essential modules assigns function to uncharacterized genes
Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, Jiang L, Chan J, Jian R, Gu M, Shcherbina A, Dubreuil MM, Spees K, Meuleman W, Snyder MP, Bassik MC, Kundaje A. Nat Genet. 2021 May;53(5):638-649. PMID: 33859415

Identification of rare and common regulatory variants in pluripotent cells using population-scale transcriptomics
Bonder MJ, Smail C, Gloudemans MJ, Frésard L, Jakubosky D, D'Antonio M, Li X, Ferraro NM, Carcamo-Orive I, Mirauta B, Seaton DD, Cai N, Vakili D, Horta D, Zhao C, Zastrow DB, Bonner DE; HipSci Consortium; iPSCORE consortium; Undiagnosed Diseases Network; PhLiPS consortium, Wheeler MT, Kilpinen H, Knowles JW, Smith EN, Frazer KA, Montgomery SB, Stegle O. Nat Genet. 2021 Mar;53(3):313-321. PMID: 33664507

Functional and structural analysis of cytokine-selective IL6ST defects that cause recessive hyper-IgE syndrome
Chen YH, Zastrow DB, Metcalfe RD, Gartner L, Krause F, Morton CJ, Marwaha S, Fresard L, Huang Y, Zhao C, McCormack C, Bick D, Worthey EA, Eng CM, Gold J; Undiagnosed Diseases Network, Montgomery SB, Fisher PG, Ashley EA, Wheeler MT, Parker MW, Shanmugasundaram V, Putoczki TL, Schmidt-Arras D, Laurence A, Bernstein JA, Griffin MDW, Uhlig HH. J Allergy Clin Immunol. 2021 Mar 23:S0091-6749(21)00471-1. PMID: 33771552

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature
Birgmeier J, Haeussler M, Deisseroth CA, Steinberg EH, Jagadeesh KA, Ratner AJ, Guturu H, Wenger AM, Diekhans ME, Stenson PD, Cooper DN, Ré C, Beggs AH, Bernstein JA, Bejerano G. Sci Transl Med. 2020 May 20;12(544):eaau9113. PMID: 32434849

AVADA: Towards Automated Pathogenic Variant Evidence Retrieval Directly from the Full Text Literature
Birgmeier J, Deisseroth CA, Hayward LE, Galhardo LMT, Tierno AP, Jagadeesh KA, Stenson PD, Cooper DN, Bernstein JA, Haeussler M, Bejerano G. Genet Med. 2020 Feb;22(2):362-370. PMID: 31467448

ClinPhen extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis
Deisseroth CA, Birgmeier J, Bodle EE, Kohler JN, Matalon DR, Nazarenko Y, Genetti CA, Brownstein CA, Schmitz-Abe K, Schoch K, Cope H, Signer R; Undiagnosed Diseases Network, Martinez-Agosto JA, Shashi V, Beggs AH, Wheeler MT, Bernstein JA, Bejerano G. Genet Med. 2019 Jul;21(7):1585-1593. PMID: 30514889

Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
Frésard L, Smail C, Ferraro NM, Teran NA, Li X, Smith KS, Bonner D, Kernohan KD, Marwaha S, Zappala Z, Balliu B, Davis JR, Liu B, Prybol CJ, Kohler JN, Zastrow DB, Reuter CM, Fisk DG, Grove ME, Davidson JM, Hartley T, Joshi R, Strober BJ, Utiramerur S; Undiagnosed Diseases Network; CareRare Canada Consortium, Lind L, Ingelsson E, Battle A, Bejerano G, Bernstein JA, Ashley EA, Boycott KM, Merker JD, Wheeler MT, Montgomery SB. Nat Med.2019 Jun;25(6):911-919. PMID: 31160820

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing
Jagadeesh KA, Paggi JM, Ye JS, Stenson PD, Cooper DN, Bernstein JA, Bejerano G. Nat Genet. 2019 Apr;51(4):755-763. PMID: 30804562

Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization
Jagadeesh KA, Birgmeier J, Guturu H, Deisseroth CA, Wenger AM, Bernstein JA, Bejerano G. Genet Med. 2019 Feb;21(2):464-470. PMID: 29997393

Effect of Genetic Diagnosis on Patients with Previously Undiagnosed Disease
Splinter K, Adams DR, Bacino CA, Bellen HJ, Bernstein JA, Cheatle-Jarvela AM, Eng CM, Esteves C, Gahl WA, Hamid R, Jacob HJ, Kikani B, Koeller DM, Kohane IS, Lee BH, Loscalzo J, Luo X, McCray AT, Metz TO, Mulvihill JJ, Nelson SF, Palmer CGS, Phillips JA 3rd, Pick L, Postlethwait JH, Reuter C, Shashi V, Sweetser DA, Tifft CJ, Walley NM, Wangler MF, Westerfield M, Wheeler MT, Wise AL, Worthey EA, Yamamoto S, Ashley EA; Undiagnosed Diseases Network. N Engl J Med.2018 Nov 29;379(22):2131-2139. PMID: 30304647

Biallelic Mutations in ATP5F1D, which Encodes a Subunit of ATP Synthase, Cause a Metabolic Disorder
Monika Oláhová, Wan Hee Yoon, Kyle Thompson, Sharayu Jangam, Liliana Fernandez, Jean M. Davidson, Jennifer E. Kyle, Megan E. Grove, Dianna G. Fisk, Jennefer N. Kohler, Matthew Holmes, Annika M. Dries, Yong Huang, Chunli Zhao, Kévin Contrepois, Zachary Zappala, Laure Frésard, Daryl Waggott, Erika M. Zink, Young-Mo Kim, Heino M. Heyman, Kelly G. Stratton, Bobbie-Jo M. Webb-Robertson, Undiagnosed Diseases Network, Michael Snyder, Jason D. Merker, Stephen B. Montgomery, Paul G. Fisher, René G. Feichtinger, Johannes A. Mayr, Julie Hall, Ines A. Barbosa, Michael A. Simpson, Charu Deshpande, Katrina M. Waters, David M. Koeller, Thomas O. Metz, Andrew A. Morris, Susan Schelley, Tina Cowan, Marisa W. Friederich, Robert McFarland, Johan L.K. Van Hove, Gregory M. Enns, Shinya Yamamoto, Euan A. Ashley, Michael F. Wangler, Robert W. Taylor, Hugo J. Bellen, Jonathan A. Bernstein, and Matthew T. Wheeler. Am J Hum Genet. 2018 Mar 1; 102(3): 494–504. PMID: 29478781

Long-read genome sequencing identifies causal structural variation in a Mendelian disease Running title: Long-read WGS identifies causal SV in a Mendelian disease
Merker JD, Wenger AM, Sneddon T, Grove M, Zappala Z, Fresard L, Waggott D, Utiramerur S, Hou Y, Smith KS, Montgomery SB, Wheeler M, Buchan JG, Lambert CC, Eng KS, Hickey L, Korlach J, Ford J, Ashley EA. Genet Med. 2018 Jan;20(1): 159-163. PMID: 28640241

Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers
Wenger AM, Guturu H, Bernstein JA, Bejerano G. Systematic reanalysis of clinical exome data yields additional diagnoses: implications for providers. Genet Med. 2017 Feb;19(2):209-214. PMID: 27441994

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity
Jagadeesh KA, Wenger AM, Berger MJ, Guturu H, Stenson PD, Cooper DN, Bernstein JA, Bejerano G. Nat Genet. 2016 Dec;48(12):1581-1586. PMID: 27776117