Impactful Results Using Genome Sequencing and Interpretation

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Our HudsonAlpha Clinical Services Lab leaders are also prolific, respected leaders in genomic research who have published dozens of scientific papers in peer-reviewed journals. These publications document the advent of age of medical genomics, discuss the growth of genomics in the clinic, and cite multiple discoveries in which genomic sequencing provided new information about the genesis of disease.

Good laboratory practice for clinical next-generation sequencing informatics pipelines.

Gargis AS1, Kalman L1, Bick DP2, da Silva C3, Dimmock DP2, Funke BH4, Gowrisankar S4, Hegde MR3, Kulkarni S5, Mason CE6, Nagarajan R7, Voelkerding KV8, Worthey EA2, Aziz N9, Barnes J10, Bennett SF11, Bisht H12, Church DM13, Dimitrova Z14, Gargis SR15, Hafez N16, Hambuch T17, Hyland FC18, Luna RA19, MacCannell D20, Mann T21, McCluskey MR22, McDaniel TK23, Ganova-Raeva LM14, Rehm HL4, Reid J24, Campo DS14, Resnick RB16, Ridge PG25, Salit ML26, Skums P14, Wong LJ24, Zehnbauer BA1, Zook JM26, Lubin IM1.

Nat Biotechnol. 2015 Jul;33(7):689-93. doi: 10.1038/nbt.3237.

 

In the absence of evidentiary harm, existing societal norms regarding parental authority should prevail.

Strong KA, Derse AR, Dimmock DP, Zusevics KL, Jeruzal J, Worthey E, Bick D, Scharer G, La Pean Kirschner A, Spellecy R, Farrell MH, Geurts J, Veith R, May T.

Am J Bioeth. 2014;14(3):24-6. doi: 10.1080/15265161.2013.879959. No abstract available.

 

Analysis and annotation of whole-genome or whole-exome sequencing-derived variants for clinical diagnosis.

Worthey EA.

Curr Protoc Hum Genet. 2013 Oct 18;79:Unit 9.24.. doi: 10.1002/0471142905.hg0924s79.

 

Whole-exome sequencing supports genetic heterogeneity in childhood apraxia of speech.

Worthey EA, Raca G, Laffin JJ, Wilk BM, Harris JM, Jakielski KJ, Dimmock DP, Strand EA, Shriberg LD.

J Neurodev Disord. 2013 Oct 2;5(1):29. doi: 10.1186/1866-1955-5-29.

 

Genomics in clinical practice: lessons from the front lines.

Jacob HJ, Abrams K, Bick DP, Brodie K, Dimmock DP, Farrell M, Geurts J, Harris J, Helbling D, Joers BJ, Kliegman R, Kowalski G, Lazar J, Margolis DA, North P, Northup J, Roquemore-Goins A, Scharer G, Shimoyama M, Strong K, Taylor B, Tsaih SW, Tschannen MR, Veith RL, Wendt-Andrae J, Wilk B,Worthey EA.

Sci Transl Med. 2013 Jul 17;5(194):194cm5. doi: 10.1126/scitranslmed.3006468.

 

Genome interpretation and assembly-recent progress and next steps.

Baker S, Joecker A, Church G, Snyder M, West J, Salzberg S, Worthey E, Smith T, Wang J, Reid JG.

Nat Biotechnol. 2012 Nov;30(11):1081-3. doi: 10.1038/nbt.2425. No abstract available.

 

Making a definitive diagnosis: successful clinical application of whole exome sequencing in a child with intractable inflammatory bowel disease.

Worthey EA, Mayer AN, Syverson GD, Helbling D, Bonacci BB, Decker B, Serpe JM, Dasu T, Tschannen MR, Veith RL, Basehore MJ, Broeckel U, Tomita-Mitchell A, Arca MJ, Casper JT, Margolis DA, Bick DP, Hessner MJ, Routes JM, Verbsky JW, Jacob HJ, Dimmock DP.

Genet Med. 2011 Mar;13(3):255-62. doi: 10.1097/GIM.0b013e3182088158.

 

A timely arrival for genomic medicine.

Mayer AN, Dimmock DP, Arca MJ, Bick DP, Verbsky JW, Worthey EA, Jacob HJ, Margolis DA.

Genet Med. 2011 Mar;13(3):195-6. doi: 10.1097/GIM.0b013e3182095089. No abstract available.

 

Exome sequencing in amyotrophic lateral sclerosis identifies risk genes and pathways.

Cirulli ET, Lasseigne BN, Petrovski S, Sapp PC, Dion PA, Leblond CS, Couthouis J, Lu YF, Wang Q, Krueger BJ, Ren Z, Keebler J, Han Y, Levy SE, Boone BE, Wimbish JR, Waite LL, Jones AL, Carulli JP, Day-Williams AG, Staropoli JF, Xin WW, Chesi A, Raphael AR, McKenna-Yasek D, Cady J, Vianney de Jong JM, Kenna KP, Smith BN, Topp S, Miller J, Gkazi A; FALS Sequencing Consortium, Al-Chalabi A, van den Berg LH, Veldink J, Silani V, Ticozzi N, Shaw CE, Baloh RH, Appel S, Simpson E, Lagier-Tourenne C, Pulst SM, Gibson S, Trojanowski JQ, Elman L, McCluskey L, Grossman M, Shneider NA, Chung WK, Ravits JM, Glass JD, Sims KB, Van Deerlin VM, Maniatis T, Hayes SD, Ordureau A, Swarup S, Landers J, Baas F, Allen AS, Bedlack RS, Harper JW, Gitler AD, Rouleau GA, Brown R, Harms MB, Cooper GM, Harris T, Myers RM, Goldstein DB.

Science. 2015 Mar 27;347(6229):1436-41. doi: 10.1126/science.aaa3650. Epub 2015 Feb 19.

 

Patterns and rates of exonic de novo mutations in autism spectrum disorders.

Neale BM, Kou Y, Liu L, Ma’ayan A, Samocha KE, Sabo A, Lin CF, Stevens C, Wang LS, Makarov V, Polak P, Yoon S, Maguire J, Crawford EL, Campbell NG, Geller ET, Valladares O, Schafer C, Liu H, Zhao T, Cai G, Lihm J, Dannenfelser R, Jabado O, Peralta Z, Nagaswamy U, Muzny D, Reid JG, Newsham I, Wu Y, Lewis L, Han Y, Voight BF, Lim E, Rossin E, Kirby A, Flannick J, Fromer M, Shakir K, Fennell T, Garimella K, Banks E, Poplin R, Gabriel S, DePristo M, Wimbish JR, Boone BE, Levy SE, Betancur C, Sunyaev S, Boerwinkle E, Buxbaum JD, Cook EH Jr, Devlin B, Gibbs RA, Roeder K, Schellenberg GD, Sutcliffe JS, Daly MJ.

Nature. 2012 Apr 4;485(7397):242-5. doi: 10.1038/nature11011

 

In sickness and in health: Context matters when considering potential benefits and risks of genome-wide sequencing. Article in Genetics in Medicine: The Official Journal of the American College of Medical Genetics 

Article: In search of rare variants: Preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes

Scott I Vrieze · Stephen M Malone · Uma Vaidyanathan · Alan Kwong · Hyun Min Kang · Xiaowei Zhan · Matthew Flickinger ·Daniel Irons · Goo Jun · Adam E Locke · Giorgio Pistis · Eleonora Porcu · Shawn Levy · Richard M Myers · William Oetting · Matt McGue · Goncalo Abecasis · William G Iacono

Nature. 2009 May 28;459(7246):569-73. doi: 10.1038/nature07953. Epub 2009 Apr 28.

 

Views of nonmedical, health system professionals regarding the return of whole genome sequencing incidental findings.

Strong KA, Zusevics KL, Bick DP, Veith R.

WMJ. 2014 Oct;113(5):179-84.

 

Ethical issues in DNA sequencing in the neonate.

Dimmock DP, Bick DP.

Clin Perinatol. 2014 Dec;41(4):993-1000. doi: 10.1016/j.clp.2014.08.016. Epub 2014 Sep 23. Review.

 

Assuring the quality of next-generation sequencing in clinical laboratory practice.

Gargis AS, Kalman L, Berry MW, Bick DP, Dimmock DP, Hambuch T, Lu F, Lyon E, Voelkerding KV, Zehnbauer BA, Agarwala R, Bennett SF, Chen B, Chin EL, Compton JG, Das S, Farkas DH, Ferber MJ, Funke BH, Furtado MR, Ganova-Raeva LM, Geigenmüller U, Gunselman SJ, Hegde MR, Johnson PL, Kasarskis A, Kulkarni S, Lenk T, Liu CS, Manion M, Manolio TA, Mardis ER, Merker JD, Rajeevan MS, Reese MG, Rehm HL, Simen BB, Yeakley JM, Zook JM, Lubin IM.

Nat Biotechnol. 2012 Nov;30(11):1033-6. doi: 10.1038/nbt.2403. No abstract available.

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