2019

Feusier, J, Watkins, WS, Thomas, J. Farrell, A, Witherspoon, DJ, Baird, L, Ha, H, Xing, J, Jorde, LB.  Pedigree-based estimation of human mobile element retrotransposition rates.   Genome Res. October 2019 29: 1567-1577; doi:10.1101/gr.247965.118

Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, JordeLB, Quinlan AR. Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. Elife. 2019 Sep 24;8. pii: e46922. doi: 10.7554/eLife.46922. PMID:31549960

Serrano MLA, Demarest BL, Tone-Pah-Hote T, Tristani-FirouziM, Yost HJ. Inhibition of Notch signaling rescues cardiovascular development in Kabuki Syndrome.  PLoS Biol. 2019 Sep 3;17(9):e3000087. doi: 10.1371/journal.pbio.3000087. eCollection 2019 Sep. PMID:31479440

Feldkamp ML, Krikov S, Gardner J, Madsen MJ, Darlington T, Sargent R, Camp NJ. Shared genomic segments in high-risk multigenerational pedigrees with gastroschisis. Birth DefectsRes. 2019 Aug 5. doi: 10.1002/bdr2.1567. [Epub ahead of print] PMID: 31385443

Chen JS, et al.Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability.G3 (Bethesda). 2018 Aug 30;8(9):2881-2888. doi: 10.1534/g3.118.200404. PMID:30166421

Nobre C, Gehlenborg N, Coon H, Lex A. Lineage: Visualizing Multivariate Clinical Data in Genealogy Graphs.  IEEE Trans Vis Comput Graph . 2019;25(3):1543–1558. doi:10.1109/TVCG.2018.281148. 

Tak CR, et al. Cost-effectiveness of early cancer surveillance for patients with Li-Fraumeni syndrome.Pediatr Blood Cancer. 2019 May;66(5):e27629. doi: 10.1002/pbc.27629. PMID:30719841

Hahn AW, et al. Germline Variant in SLCO2B1and Response to Abiraterone Acetate Plus Prednisone (AA) in New-onset Metastatic Castration-resistant Prostate Cancer(mCRPC).Mol Cancer Ther. 2019 Mar;18(3):726-729. doi: 10.1158/1535-7163.MCT-18-0739. PMID:30587554

2018 

Wei X, et al. Germline Lysine-Specific Demethylase 1 (LSD1/KDM1A) Mutations Confer Susceptibility to Multiple Myeloma. Cancer Res. 2018 May 15;78(10):2747-2759. doi: 10.1158/0008-5472.CAN-17-1900. Epub 2018 Mar 20. PubMed PMID: 29559475; PubMed Central PMCID: PMC5955848. 

Coon H, et al. Genome-wide significant regions in 43 Utah high-risk families implicate multiple genes involved in risk for completed suicide. Mol Psychiatry. 2018. doi: 10.1038/s41380-018-0282-3. PubMed PMID: 30353169.

Jurynec MJ, Sawitzke AD, Beals TC, Redd MJ, Stevens J, Otterud B, Leppert MF, Grunwald DJ. A hyperactivating proinflammatory RIPK2 allele associated with early-onset osteoarthritis. Hum Mol Genet. 2018 Jul 1;27(13):2383-2391. doi: 10.1093/hmg/ddy132. Erratum in: Hum Mol Genet. 2018 Jul 1;27(13):2406.  PMID: 29659823

Kleinstern G, et al. Association of polygenic risk score with the risk of chronic lymphocytic leukemia and monoclonal B-cell lymphocytosis.Blood. 2018;131(23):2541-51. doi: 10.1182/blood-2017-11-814608. PubMed PMID: 29674426; PMCID: PMC5992865

Waller RG, et al. Novel pedigree analysis implicates DNA repair and chromatin remodeling in multiple myeloma risk. PLoS Genet. 2018;14(2):e1007111. doi: 10.1371/journal.pgen.1007111. PubMed PMID: 29389935; PMCID: PMC5794067.

Yu Y, et al. XPAT: a toolkit to conduct cross-platform association studies with heterogeneous sequencing datasets. Nucleic Acids Res. 2018Apr 6;46(6):e32. doi: 10.1093/nar/gkx1280. PubMed PMID: 29294048; PubMed Central PMCID: PMC5888834.

Matsunmi N, et al.Germline but not somatic de novo mutations are common in human congenital diaphragmatic hernia.Birth Defects Res. 2018 Apr 17;110(7):610-617. doi: 10.1002/bdr2.1223. PMID: 29570242

Wooderchak-Donahue, W. L., et al. 2018. Genome sequencing reveals a deep intronic splicing ACVRL1 mutation hotspot in Hereditary Haemorrhagic Telangiectasia, J Med Genet.

Than, H., Y. Qiao, X. Huang, D. Yan, J. S. Khorashad, A. D. Pomicter, T. J. Kovacsovics, G. T. Marth, T. O'Hare, and M. W. Deininger. 2018.Ongoing clonal evolution in chronic myelomonocytic leukemia on hypomethylating agents: a computational perspective, Leukemia, 32: 2049-54.

Teerlink, C. C., et al. 2018. A Nonsynonymous Variant in the GOLM1 Gene in Cutaneous Malignant Melanoma, J Natl Cancer Inst.

Leiding JW, et al. Inborn Errors Working Party of the European Society for Blood and Marrow Transplantation and the Primary Immune Deficiency Treatment Consortium. Hematopoietic stem cell transplantation in patients with gain-of-function signal transducer and activator of transcription 1 mutations.J Allergy Clin Immunol. 2018Feb;141(2):704-717.e5. doi: 10.1016/j.jaci.2017.03.049. PubMed PMID: 28601685.

Young EL, et al. Pancreatic cancer as a sentinel for hereditary cancer predispositionBMC Cancer. 2018 Jun 27;18(1):697. PMID: 29945567

Ostrander, B. E. P., et al. 2018. Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy, NPJ Genom Med, 3: 22.

Chen, J. S., F. Hu, S. Kugathasan, L. B. Jorde, D. Nix, A. Rutherford, L. Denson, W. S. Watkins, S. Prahalad, C. Huff, and S. L. Guthery. 2018. Targeted Gene Sequencing in Children with Crohn's Disease and Their Parents: Implications for Missing Heritability, G3 (Bethesda), 8: 2881-88.

Manuck TA, et al. Eunice Kennedy Shriver National Institute of Child H, Human Development G, Proteomics Network for Preterm Birth R. Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth: a case-control study. BJOG. 2018;125(3):343-50. doi: 10.1111/1471-0528.14485. PubMed PMID: 28139890. 

Al-Agha AE, et al. Primary Ovarian Insufficiency and Azoospermia in Carriers of a Homozygous PSMC3IP Stop Gain Mutation. J Clin Endocrinol Metab. 2018;103(2):555-63. doi: 10.1210/jc.2017-01966. PubMed PMID: 29240891; PMCID: PMC5800840.

Peron A, et al.TSC Study Group of the San Paolo Hospital of Milan. Deep phenotyping of patients with Tuberous Sclerosis Complex and no mutation identified in TSC1 and TSC2. Eur J Med Genet. 2018 Jul;61(7):403-410. doi: 10.1016/j.ejmg.2018.02.005. Epub 2018 Feb 9. PMID:29432982 

2017

Bloom JL, Lin C, Imundo L, Guthery S, Stepenaskie S, Galambos C, Lowichik A, Bohnsack JF. H syndrome: 5 new cases from the United States with novel features and responses to therapy.Pediatr Rheumatol Online J. 2017Oct 17;15(1):76. doi: 10.1186/s12969-017-0204-y. PubMed PMID: 29041934; PubMed Central PMCID: PMC5645937. 

Feng, Bing-Jian. “PERCH: A Unified Framework for Disease Gene Prioritization.” Human mutation vol. 38,3 (2017): 243-251. doi:10.1002/humu.23158

Gibson SB, Downie JM, Tsetsou S, Feusier JE, Figueroa KP, Bromberg MB, Jorde LB, Pulst SM. The evolving genetic risk for sporadic ALS.Neurology. 2017;89(3):226-33. doi: 10.1212/WNL.0000000000004109. PubMed PMID: 28642336; PMCID: PMC551381. 

Ward A, Karren MA, Di Sera T, Miller C, Velinder M, Qiao Y, Filloux FM, OstranderB, ButterfieldR, Bonkowsky JL, Dere W, Marth GT. Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobioweb tools.J Clin Transl Sci. 2017 Dec;1(6):381-386. PMID:29707261

Jin SC, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands.Nat Genet. 2017;49(11):1593-601. doi: 10.1038/ng.3970. PubMed PMID: 28991257; PMCID: PMC5675000.

Brady SW, et al. Combating subclonal evolution of resistant cancer phenotypes.Nat Commun. 2017;8(1):1231. doi: 10.1038/s41467-017-01174-3. PubMed PMID: 29093439; PMCID: PMC5666005.

Hu H, Petousi N, Glusman G, Yu Y, Bohlender R, Tashi T, et al. (2017) Evolutionary history of Tibetans inferred from whole-genome sequencing. PLoS Genet 13(4): e1006675. https://doi.org/10.1371/journal.pgen.1006675

Moriwaki M, Moore B, Mosbruger T, Neklason DW, Yandell M, Jorde LB, Welt C (2017). POLR2C Mutations are Associated with Primary Ovarian Insufficiency in Women. J Endocr Soc, 1(3), 162-173.

2016

Chapman, N. H. et alWhole exome sequencing in extended families with autism spectrum disorder implicates four candidate genesHuman genetics 134, 1055-1068, doi:10.1007/s00439-015-1585-y (2016).

Graf, E. H. et alUnbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR PanelJournal of clinical microbiology 54, 1000-1007, doi:10.1128/JCM.03060-15 (2016).

Hasstedt, S. J., Coon, H., Xin, Y., Adams, T. D. & Hunt, S. C. APOH interacts with FTO to predispose to healthy thinnessHuman genetics 135, 201-207, doi:10.1007/s00439-015-1629-3 (2016).

Kuehn, H. S. et alLoss of B Cells in Patients with Heterozygous Mutations in IKAROSN Engl J Med 374, 1032-1043, doi:10.1056/NEJMoa1512234 (2016).

Layer, R. M., Kindlon, N., Karczewski, K. J., Exome Aggregation, C. & Quinlan, A. R. Efficient genotype compression and analysis of large genetic-variation data setsNature methods 13, 63-65, doi:10.1038/nmeth.3654 (2016).

Mason, C. C. et alAge-related mutations and chronic myelomonocytic leukemiaLeukemia 30, 906-913, doi:10.1038/leu.2015.337 (2016).

Young, E. L. et alMultigene testing of moderate-risk genes: be mindful of the missenseJ Med Genet, doi:jmedgenet-2015-103398 (2016)

2015

Addis, L. et alMicrodeletions of ELP4 Are Associated with Language Impairment, Autism Spectrum Disorder, and Mental RetardationHum Mutat 36, 842-850, doi:10.1002/humu.22816 (2015).

Bowles, N. E. et alExome analysis of a family with Wolff-Parkinson-White syndrome identifies a novel disease locusAmerican journal of medical genetics. Part A167, 2975-2984, doi:10.1002/ajmg.a.37297 (2015).

Buchbinder, D. et alIdentification of patients with RAG mutations previously diagnosed with common variable immunodeficiency disordersJ Clin Immunol 35, 119-124, doi:10.1007/s10875-014-0121-5 (2015).

Kronenberg, Z. N. et alWham: Identifying Structural Variants of Biological ConsequencePLoS computational biology 11, e1004572, doi:10.1371/journal.pcbi.1004572 (2015).

Lee, W. P., Wu, J. & Marth, G. T. Toolbox for mobile-element insertion detection on cancer genomesCancer informatics 14, 37-44, doi:10.4137/CIN.S24657 (2015).

Lindberg, M. R., Hall, I. M. & Quinlan, A. R. Population-based structural variation discovery with Hydra-MultiBioinformatics31, 1286-1289, doi:10.1093/bioinformatics/btu771 (2015).

Nash, D. et alShared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR)PloS one 10, e0131514, doi:10.1371/journal.pone.0131514 (2015).

Welch, B. M., Dere, W. & Schiffman, J. D. Family Health History: The Case for Better ToolsJama, doi:10.1001/jama.2015.2417 (2015).

Wu, W. et alThe heritability of gestational age in a two-million member cohort: implications for spontaneous preterm birthHuman genetics, doi:10.1007/s00439-015-1558-1 (2015).

2014

Chen, K. et alAutoimmunity due to RAG deficiency and estimated disease incidence in RAG1/2 mutationsThe Journal of allergy and clinical immunology 133, 880-882 e810, doi:10.1016/j.jaci.2013.11.038 (2014).

Darlington, T. M. et alIdentifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthmaTransl Psychiatry 4, e471, doi:10.1038/tp.2014.111 (2014).

Gibson, S. B., Figueroa, K. P., Bromberg, M. B., Pulst, S. M. & Cannon-Albright, L. Familial clustering of ALS in a population-based resourceNeurology82, 17-22, doi:10.1212/01.wnl.0000438219.39061.da (2014). 

Hu, H. et alA unified test of linkage analysis and rare-variant association for analysis of pedigree sequence dataNat Biotechnol 32, 663-669, doi:10.1038/nbt.2895 (2014).

Kennedy, B. et alUsing VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing DataCurr Protoc Hum Genet 81, 6 14 11-16 14 25, doi:10.1002/0471142905.hg0614s81 (2014).

Layer, R. M., Chiang, C., Quinlan, A. R. & Hall, I. M. LUMPY: a probabilistic framework for structural variant discoveryGenome biology 15, R84, doi:10.1186/gb-2014-15-6-r84 (2014).

Lee, W. P. et alMOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mappingPloS one 9, e90581, doi:10.1371/journal.pone.0090581 (2014).

Lee, W. P., Wu, J. & Marth, G. T. Toolbox for mobile-element insertion detection on cancer genomesCancer informatics 13, 45-52, doi:10.4137/CIN.S13979 (2014). 

Manuck, T. A. et alPharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth preventionAmerican journal of obstetrics and gynecology 210, 321 e321-321 e321, doi:10.1016/j.ajog.2014.01.013 (2014). 

Miller, C. A., Qiao, Y., DiSera, T., D'Astous, B. & Marth, G. T. bam.iobio: a web-based, real-time, sequence alignment file inspectorNature methods 11, 1189, doi:10.1038/nmeth.3174 (2014).

Park, D. J. et alRare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancersCancer Discov 4, 804-815, doi:10.1158/2159-8290.CD-14-0212 (2014).

Qiao, Y. et alSubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritizationGenome biology 15, 443, doi:10.1186/s13059-014-0443-x (2014).

Quinlan, A. R. BEDTools: The Swiss-Army Tool for Genome Feature AnalysisCurrent protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]47, 11 12 11-34, doi:10.1002/0471250953.bi1112s47 (2014).

Singleton, M. V. et alPhevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear familiesAm J Hum Genet94, 599-610, doi:10.1016/j.ajhg.2014.03.010 (2014).

Wu, J. et alTangram: a comprehensive toolbox for mobile element insertion detectionBMC genomics15, 795, doi:10.1186/1471-2164-15-795 (2014).

Pre-2014

Chen, K. et alGermline mutations in NFKB2 implicate the noncanonical NF-kappaB pathway in the pathogenesis of common variable immunodeficiencyAm J Hum Genet 93, 812-824, doi:10.1016/j.ajhg.2013.09.009 (2013).

Coonrod, E. M., Margraf, R. L., Russell, A., Voelkerding, K. V. & Reese, M. G. Clinical analysis of genome next-generation sequencing data using the Omicia platformExpert Rev Mol Diagn 13, 529-540, doi:10.1586/14737159.2013.811907 (2013).

Hu, H. et alVAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrixGenet Epidemiol 37, 622-634, doi:10.1002/gepi.21743 (2013). 

Paila, U., Chapman, B. A., Kirchner, R. & Quinlan, A. R. GEMINI: integrative exploration of genetic variation and genome annotationsPLoS computational biology 9, e1003153, doi:10.1371/journal.pcbi.1003153 (2013).

Cancer Genome Atlas, N. Comprehensive molecular characterization of human colon and rectal cancerNature 487, 330-337, doi:10.1038/nature11252 (2012). 

Knight, S. et alShared genomic segment analysis: the power to find rare disease variantsAnn Hum Genet 76, 500-509, doi:10.1111/j.1469-1809.2012.00728.x (2012).

McDonald, S. A. et alComprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositoriesAm J Clin Pathol 138, 31-41, doi:10.1309/AJCPXBA69LNSCVMH (2012).

Stein, E. A. et alEffect of a monoclonal antibody to PCSK9 on LDL cholesterolN Engl J Med 366, 1108-1118, doi:10.1056/NEJMoa1105803 (2012).

Feng, B. J., Tavtigian, S. V., Southey, M. C. & Goldgar, D. E. Design considerations for massively parallel sequencing studies of complex human diseasePloS one 6, e23221, doi:10.1371/journal.pone.0023221 (2011).

Rope, A. F. et alUsing VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiencyAm J Hum Genet 89, 28-43, doi:10.1016/j.ajhg.2011.05.017 (2011). 

Yandell, M. et alA probabilistic disease-gene finder for personal genomesGenome Res 21, 1529-1542, doi:10.1101/gr.123158.111 (2011). 

Roach, J. C. et alAnalysis of genetic inheritance in a family quartet by whole-genome sequencingScience328, 636-639, doi:10.1126/science.1186802 (2010). 

Kerber, R. A., Amos, C. I., Yeap, B. Y., Finkelstein, D. M. & Thomas, D. C. Design considerations in a sib-pair study of linkage for susceptibility loci in cancerBMC Med Genet9, 64, doi:10.1186/1471-2350-9-64 (2008).