Publications

2016

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

Graf, E. H. et al. Unbiased Detection of Respiratory Viruses by Use of RNA Sequencing-Based Metagenomics: a Systematic Comparison to a Commercial PCR Panel. Journal of clinical microbiology54, 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 thinness. Human genetics135, 201-207, doi:10.1007/s00439-015-1629-3 (2016).

Kuehn, H. S. et al. Loss of B Cells in Patients with Heterozygous Mutations in IKAROS. N Engl J Med374, 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 sets. Nature methods13, 63-65, doi:10.1038/nmeth.3654 (2016).

Mason, C. C. et al. Age-related mutations and chronic myelomonocytic leukemia. Leukemia30, 906-913, doi:10.1038/leu.2015.337 (2016).

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

2015

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

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

Buchbinder, D. et al. Identification of patients with RAG mutations previously diagnosed with common variable immunodeficiency disorders. J Clin Immunol35, 119-124, doi:10.1007/s10875-014-0121-5 (2015).

Kronenberg, Z. N. et al. Wham: Identifying Structural Variants of Biological Consequence. PLoS computational biology11, e1004572, doi:10.1371/journal.pcbi.1004572 (2015).

Lee, W. P., Wu, J. & Marth, G. T. Toolbox for mobile-element insertion detection on cancer genomes. Cancer informatics14, 37-44, doi:10.4137/CIN.S24657 (2015).

Lindberg, M. R., Hall, I. M. & Quinlan, A. R. Population-based structural variation discovery with Hydra-Multi. Bioinformatics31, 1286-1289, doi:10.1093/bioinformatics/btu771 (2015).

Nash, D. et al. Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR). PloS one10, e0131514, doi:10.1371/journal.pone.0131514 (2015).

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

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

2014

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

Darlington, T. M. et al. Identifying rare variants for genetic risk through a combined pedigree and phenotype approach: application to suicide and asthma. Transl Psychiatry4, 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 resource. Neurology82, 17-22, doi:10.1212/01.wnl.0000438219.39061.da (2014).

Hu, H. et al. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data. Nat Biotechnol32, 663-669, doi:10.1038/nbt.2895 (2014).

Kennedy, B. et al. Using VAAST to Identify Disease-Associated Variants in Next-Generation Sequencing Data. Curr Protoc Hum Genet81, 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 discovery. Genome biology15, R84, doi:10.1186/gb-2014-15-6-r84 (2014).

Lee, W. P. et al. MOSAIK: a hash-based algorithm for accurate next-generation sequencing short-read mapping. PloS one9, e90581, doi:10.1371/journal.pone.0090581 (2014).

Lee, W. P., Wu, J. & Marth, G. T. Toolbox for mobile-element insertion detection on cancer genomes. Cancer informatics13, 45-52, doi:10.4137/CIN.S13979 (2014).

Manuck, T. A. et al. Pharmacogenomics of 17-alpha hydroxyprogesterone caproate for recurrent preterm birth prevention. American journal of obstetrics and gynecology210, 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 inspector. Nature methods11, 1189, doi:10.1038/nmeth.3174 (2014).

Park, D. J. et al. Rare mutations in RINT1 predispose carriers to breast and Lynch syndrome-spectrum cancers. Cancer Discov4, 804-815, doi:10.1158/2159-8290.CD-14-0212 (2014).

Qiao, Y. et al. SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization. Genome biology15, 443, doi:10.1186/s13059-014-0443-x (2014).

Quinlan, A. R. BEDTools: The Swiss-Army Tool for Genome Feature Analysis. Current 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 al. Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. Am J Hum Genet94, 599-610, doi:10.1016/j.ajhg.2014.03.010 (2014).

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

Pre-2014

Chen, K. et al. Germline mutations in NFKB2 implicate the noncanonical NF-kappaB pathway in the pathogenesis of common variable immunodeficiency. Am 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 platform. Expert Rev Mol Diagn13, 529-540, doi:10.1586/14737159.2013.811907 (2013).

Hu, H. et al. VAAST 2.0: improved variant classification and disease-gene identification using a conservation-controlled amino acid substitution matrix. Genet Epidemiol37, 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 annotations. PLoS computational biology9, e1003153, doi:10.1371/journal.pcbi.1003153 (2013).

Cancer Genome Atlas, N. Comprehensive molecular characterization of human colon and rectal cancer. Nature487, 330-337, doi:10.1038/nature11252 (2012).

Knight, S. et al. Shared genomic segment analysis: the power to find rare disease variants. Ann Hum Genet76, 500-509, doi:10.1111/j.1469-1809.2012.00728.x (2012).

McDonald, S. A. et al. Comprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositories. Am J Clin Pathol138, 31-41, doi:10.1309/AJCPXBA69LNSCVMH (2012).

Stein, E. A. et al. Effect of a monoclonal antibody to PCSK9 on LDL cholesterol. N Engl J Med366, 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 disease. PloS one6, e23221, doi:10.1371/journal.pone.0023221 (2011).

Rope, A. F. et al. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet89, 28-43, doi:10.1016/j.ajhg.2011.05.017 (2011).

Yandell, M. et al. A probabilistic disease-gene finder for personal genomes. Genome Res21, 1529-1542, doi:10.1101/gr.123158.111 (2011).

Roach, J. C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science328, 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 cancer. BMC Med Genet9, 64, doi:10.1186/1471-2350-9-64 (2008).