Resources

Publications

Chasing a moving target: Detection of mitochondrial heteroplasmy for clinical diagnostics
White EJ, Ross T, Lopez E, Nikiforov A, Gault C, Batorsky R, Darcy C, Campagna D, Fleming M, Thompson JF. bioRxiv 222109 (2017)

Orthogonal NGS for Clinical Diagnostics.
Chennagiri N, White EJ, Frieden A, Lopez E, Lieber DS, Nikiforov A, Ross T, Batorsky R, Hansen S, Lip V, Luquette LJ, Mauceli E, Margulies D, Milos PM, Napolitano N, Nizzari MM, Yu T, Thompson JF. Scientific Reports 6, Article number: 24650 (2016)

Somatic mutations in cerebral cortical malformations.
Jamuar SS, Lam AT, Kircher M, D’Gama AM, Wang J, Barry BJ, Zhang X, Hill RS, Partlow JN, Rozzo A, Servattalab S, Mehta BK, Topcu M, Amrom D, Andermann E, Dan B, Parrini E, Guerrini R, Scheffer IE, Berkovic SF, Leventer RJ, Shen Y, Wu BL, Barkovich AJ, Sahin M, Chang BS, Bamshad M, Nickerson DA, Shendure J, Poduri A,Yu TW, Walsh CA. N Engl J Med. 2014;371(8):733-43.

Recurrent 8q13.2-13.3 microdeletions associated with Branchio-oto-renal syndrome are mediated by human endogenous retroviral (HERV) sequence blocks.
Chen X, Wang J, Mitchell E, Guo J, Wang L, Zhang Y, Hodge JC, Shen Y. BMC Med Genet. 2014; 15(1):90.

Novel Variant in CDKN1C Is Associated With Intrauterine Growth Restriction, Short Stature, and Early-Adulthood-Onset Diabetes.
Kerns SL, Guevara-Aguirre J, Andrew S, Geng J, Guevara C, Guevara-Aguirre M, Guo M, Oddoux C, Shen Y, Zurita A, Rosenfeld RG, Ostrer H, Hwa V, Dauber A. A  J Clin Endocrinol Metab. 2014; 99(10):E2117-22.

The Rapidly Emerging Role for Whole Exome Sequencing in Clinical Genetics.
Shen Y, Lopez R Milos PMM. Curr Genet Med Rep 2014; 2:103–112.

Whole exome sequencing to identify genetic causes of short stature.
Guo MH, Shen Y, Walvoord EC, Miller TC, Moon JE, Hirschhorn JN, Dauber A. Horm Res Paediatr. 2014;82(1):44-52.

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.
SEQC/MAQC-III Consortium; SEQC/MAQC-III Consortium. Nat Biotechnol. 2014;32(9):903-14.

Copy number variation plays an important role in clinical epilepsy.
Olson H, Shen Y, Avallone J, et al. Ann Neurol. 2014; 75(6):943-58.

Dystrophin is a tumor suppressor in human cancers with myogenic programs.
Wang Y, Marino-Enriquez A, Bennett RR, Zhu M, Shen Y, Eilers G, Lee JC, Henze J, Fletcher BS, Gu Z, Fox EA, Antonescu CR, Fletcher CD, Guo X, Raut CP, Demetri GD, van de Rijn M, Ordog T, Kunkel LM, Fletcher JA. Nat Genet. 2014; 46(6):601-6.

Familial 46,XY sex reversal without campomelic dysplasia caused by a deletion upstream of the SOX9 gene.
Bhagavath B, Layman LC, Ullmann R, Shen Y, Ha K, Rehman K, Looney S, McDonough PG, Kim HG, Carr BR. Mol Cell Endocrinol. 2-14;393(1-2):1-7.

LIN28 is involved in glioma carcinogenesis and predicts outcomes of glioblastoma multiform patients.
Qin R, Zhou J, Chen C, Xu T, Yan Y, Ma Y, Zheng Z, Shen Y, Lu Y, Fu D, Chen J. PLoS One. 2014; 9(1):e86446.

Spectrum of genes involved in a unique case of Potocki Schaffer syndrome with a large chromosome 11 deletion.
Romeike BF, Shen Y, Nishimoto HK, Morton CC, Layman LC, Kim HG. Clin Neuropathol. 2014; 33(3):238-44.

Novel frame-shift mutations of GLI3 gene in non-syndromic postaxial polydactyly patients.
Wang Z, Wang J, Li Y, Geng J, Fu Q, Xu Y, Shen Y. (2014) Novel frame-shift mutations of GLI3 gene in non-syndromic postaxial polydactyly patients. Clin Chim Acta. 433:195-9.

Mutations in HFM1 in Recessive Primary Ovarian Insufficiency.
Wang J, Zhang WX, Jiang H, Wu BL. N Engl J Med. 2014;370(10):972-4.

Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes
Lionel AC, Tammimies K, Vaags AK, et al. Hum Mol Genet. 2014; 23(10):2752-68.

Mutations in epigenetic regulators including SETD2 are gained during relapse in paediatric acute lymphoblastic leukaemia.
Mar BG, Bullinger LB, McLean KM, Grauman PV, Harris MH, Stevenson K, Neuberg DS, Sinha AU, Sallan SE, Silverman LB, Kung AL, Lo Nigro L, Ebert BL, Armstrong SA. Nat Commun.  2014; 5:3469.

When a “disease-causing mutation” is not a pathogenic variant.
Wang J, Shen Y. Clin Chem. 2014; 60(5):711-3.

A novel deletion of IGF1 in a patient with idiopathic short stature provides insight Into IGF1 haploinsufficiency.
Batey L, Moon JE, Yu Y, Wu B, Hirschhorn JN, Shen Y, Dauber A. J Clin Endocrinol Metab. 2014; 99(1):E153-9.

c-Myc inhibition prevents leukemia initiation in mice and impairs the growth of relapsed and induction failure pediatric T-ALL cells.
Roderick JE, Tesell J, Shultz LD, Brehm MA, Greiner DL, Harris MH, Silverman LB, Sallan SE, Gutierrez A, Look AT, Qi J, Bradner JE, Kelliher MA. Blood. 2014; 123(7):1040-50

Future of clinical genomics in pediatric oncology.
Janeway KA, Place AE, Kieran MW, Harris MH. 2014; 31(15):1893-903

Mutation of KCNJ8 in a patient with Cantu syndrome with unique vascular abnormalities – support for the role of K(ATP) channels in this condition.
Brownstein CA, Towne MC, Luquette LJ, Harris DJ, Marinakis NS, Meinecke P, Kutsche K, Campeau PM, Yu TW, Margulies DM, Agrawal PB, Beggs AH. Eur J Med Genet. 2013 Dec;56(12):678-82.

Exome sequencing identifies a novel SMCHD1 mutation in facioscapulohumeral muscular dystrophy 2.
Mitsuhashi S, Boyden SE, Estrella EA, Jones TI, Rahimov F, Yu TW, Darras BT, Amato AA, Folkerth RD, Jones PL, Kunkel LM, Kang PB. Neuromuscul Disord. 2013 Dec;23(12):975-80.

Landscape of genomic alterations in cervical carcinomas.
Ojesina AI, Lichtenstein L, Freeman SS, et al. Nature 2013 Dec 25 (EPUB).

Disruption of a large intergenic noncoding RNA in subjects with neurodevelopmental disabilities.
Talkowski ME, Maussion G, Crapper L, Rosenfeld JA, Blumenthal I, Hanscom C, Chiang C, Lindgren A, Pereira S, Ruderfer D, Diallo AB, Lopez JP, Turecki G, Chen ES, Gigek C, Harris DJ, Lip V, An Y, Biagioli M, Macdonald ME, Lin M, Haggarty SJ, Sklar P, Purcell S, Kellis M, Schwartz S, Shaffer LG, Natowicz MR, Shen Y, Morton CC, Gusella JF, Ernst C. Am J Hum Genet. 2012 Dec 7; 91(6):1128-34.

Identification of KLHL41 Mutations Implicates BTB-Kelch-Mediated Ubiquitination as an Alternate Pathway to Myofibrillar Disruption in Nemaline Myopathy.
Gupta VA, Ravenscroft G, Shaheen R, Todd EJ, Swanson LC, Shiina M, Ogata K,Hsu C, Clarke NF, Darras BT, Farrar MA, Hashem A, Manton ND, Muntoni F, North KN, Sandaradura SA, Nishino I, Hayashi YK, Sewry CA, Thompson EM, Yau KS, Brownstein CA, Yu TW, Allcock RJ, Davis MR, Wallgren-Pettersson C, Matsumoto N, Alkuraya FS, Laing NG, Beggs AH. Am J Hum Genet. 2013 Dec 5;93(6):1108-17.

Highly penetrant alterations of a critical region including BDNF in human psychopathology and obesity.
Ernst C, Marshall CR, Shen Y, Metcalfe K, Rosenfeld J, Hodge JC, Torres A, Blumenthal I, Chiang C, Pillalamarri V, Crapper L, Diallo AB, Ruderfer D, Pereira S, Sklar P, Purcell S, Wildin RS, Spencer AC, Quade BF, Harris DJ, Lemyre E, Wu BL, Stavropoulos DJ, Geraghty MT, Shaffer LG, Morton CC, Scherer SW, Gusella JF, Talkowski ME. Arch Gen Psychiatry. 2012 Dec 1; 69(12):1238-46.

Association between MTHFR Gene Polymorphisms and the Risk of Autism Spectrum Disorders: A Meta-Analysis.
Pu D, Shen Y, Wu J. Autism Res. 2013 Oct; 6(5):384-92.

Adjusting head circumference for covariates in autism: clinical correlates of a highly heritable continuous trait.
Chaste P, Klei L, Sanders SJ, Murtha MT, Hus V, Lowe JK, Willsey AJ, Moreno-De-Luca D, Yu TW, Fombonne E, Geschwind D, Grice DE, Ledbetter DH, Lord C, Mane SM, Lese Martin C, Martin DM, Morrow EM, Walsh CA, Sutcliffe JS, State MW, Devlin B, Cook EH Jr, Kim SJ. Biol Psychiatry. 2013 Oct 15;74(8):576-84.

Somatic alterations contributing to metastasis of a castration-resistant prostate cancer.
Nickerson ML, Im KM, Misner KJ, Tan W, Lou H, Gold B, Wells DW, Bravo HC, Fredrikson KM, Harkins TT, Milos P, Zbar B, Linehan WM, Yeager M, Andresson T, Dean M, Bova GS. Hum Mutat. 2013 Sep;34(9):1231-41.

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.
Cross-Disorder Group of the Psychiatric Genomics Consortium, Lee SH, Ripke S, Neale BM, et al. Nat Genet. 2013 Sep;45(9):984-94.

Density matters: comparison of array platforms for detection of copy-number variation and copy-neutral abnormalities.
Mason-Suares H, Kim W, Grimmett L, Williams ES, Horner VL, Kunig D, Goldlust IS, Wu BL, Shen Y, Miller DT, Martin CL, Rudd MK. Genet Med. 2013 Sep;15(9):706-12.

Delayed puberty and estrogen resistance in a woman with estrogen receptor a variant.
Quaynor SD, Stradtman EW, Kim HG, Shen Y, Chorich LP, Schreihofer DA, Layman LC. N Engl J Med. 2013 Jul 11; 369(2):164-71.

SOX12 and NRSN2 are candidate genes for 20p13 subtelomeric deletions associated with developmental delay.
An Y, Amr SS, Torres A, Weissman L, Raffalli P, Cox G, Sheng X, Lip V, Bi W, Patel A, Stankiewicz P, Wu BL, Shen Y. Am J Med Genet B Neuropsychiatr Genet. 2013 Sep 6.

On the importance of small changes in RNA expression.
St Laurent G, Shtokalo D, Tackett MR, Yang Z, Vyatkin Y, Milos PM, Seilheimer B, McCaffrey TA, Kapranov P. Methods. 2013 Sep 1;63(1):18-24.

Screening for Coding Variants in FTO and SH2B1 Genes in Chinese Patients with Obesity.
Zheng Z, Hong L, Huang X, Yang P, Li J, Ding Y, Yao RE, Geng J, Shen Y, Shen Y, Fu Q, Yu Y. PLoS One. 2013; 8(6):e67039.

Neurologic features of Hutchinson-Gilford progeria syndrome after lonafarnib treatment.
Ullrich NJ, Kieran MW, Miller DT, Gordon LB, Cho YJ, Silvera VM, Giobbie-Hurder A, Neuberg D, Kleinman ME. Neurology. 2013 Jul 30;81(5):427-30.

Mutational heterogeneity in cancer and the search for new cancer-associated genes.
Lawrence MS, Stojanov P, Polak P, et al. Nature. 2013 Jul 11.

Increased genome instability in human DNA segments with self-chains: homology-induced structural variations via replicative mechanisms.
Zhou W, Zhang F, Chen X, Shen Y, Lupski JR, Jin L. Hum Mol Genet. 2013 Jul 1;22(13):2642-51.

Contribution of copy number variants involving nonsense-mediated mRNA decay pathway genes to neuro-developmental disorders.
Nguyen LS, Kim HG, Rosenfeld JA, Shen Y, Gusella JF, Lacassie Y, Layman LC, Shaffer LG, Gécz J. Hum Mol Genet. 2013 May 1; 22(9):1816-25.

Fine-Mapping of Restless Legs Locus 4 (RLS4) Identifies a Haplotype over the SPATS2L and KCTD18 Genes.
Pichler I, Schwienbacher C, Zanon A, Fuchsberger C, Serafin A, Facheris MF, Marroni F, Pattaro C, Shen Y, Tellgren-Roth C, Gyllensten U, Gusella JF, Hicks AA, Pramstaller PP. J Mol Neurosci. 2013 Mar; 49(3):600-5.

Molecular Analysis of a Deletion Hotspot in the NRXN1 Region Reveals the Involvement of Short Inverted Repeats in Deletion CNVs.
Chen X, Shen Y, Zhang F, Chiang C, Pillalamarri V, Blumenthal I, Talkowski M, Wu BL, Gusella JF. Am J Hum Genet. 2013 Mar 7; 92(3):375-86.

Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors.
Chmielecki J, Crago AM, Rosenberg M, O’Connor R, Walker SR, Ambrogio L, Auclair D, McKenna A, Heinrich MC, Frank DA, Meyerson M. Nat Genet. 2013 Feb.

Exonic Deletions in AUTS2 Cause a Syndromic Form of Intellectual Disability and Suggest a Critical Role for the C Terminus.
Beunders G, Voorhoeve E, Golzio C, et al. Am J Hum Genet. 2013 Feb 7; 92(2):210-20.

GAP-43 dependency defines distinct effects of netrin-1 on cortical and spinal neurite outgrowth and directional guidance.
Shen Y, Meiri K. Int J Dev Neurosci. 2013 Feb; 31(1):11-20.

Chromosomal microarray impacts clinical management.
Riggs E, Wain K, Riethmaier D, Smith-Packard B, Faucett W, Hoppman N, Thorland E, Patel V, Miller D. Clin Genet. 2013 Jan 25.

Using whole-exome sequencing to identify inherited causes of autism.
Yu TW, Chahrour MH, Coulter ME, et al. Neuron. 2013 Jan 23;77(2):259-73.

MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32.
Kelly AD, Haibe-Kains B, Janeway KA, Hill KE, Howe E, Goldsmith J, Kurek K, Perez-Atayde AR, Francoeur N, Fan JB, April C, Schneider H, Gebhardt MC, Culhane A, Quackenbush J, Spentzos D. Genome Med. 2013 Jan 22;5(1):2.

Detection of copy number variants reveals association of cilia genes with neural tube defects.
Chen X, Shen Y, Gao Y, Zhao H, Sheng X, Zou J, Lip V, Xie H, Guo J, Shao H, Bao Y, Shen J, Niu B, Gusella JF, Wu BL, Zhang T. PLoS One. 2013;8(1):e54492.

Exonic Deletions in AUTS2 Cause a Syndromic Form of Intellectual Disability and Suggest a Critical Role for the C Terminus.
Beunders G, Voorhoeve E, Golzio C, et al. Am J Hum Genet. 2013 Jan 15.

Presentations

Tim Yu presents a webinar entitled "Clinical Exome Sequencing: When Is It Appropriate And What To Look For." October 2015.

Tim Yu Next-Generation Human Genomics 2013

Tim Yu NSGC Keynote 2013

Patrice Milos BioConference Live August 2013

Yiping Shen ACMG 2014

Video- Patrice Milos Claritas Genomics: The Future of Pediatric Diagnostics is Now

Video- Elizabeth Boudreau discusses using Amazon Web Services to improve Claritas's operational efficiency

Posters

Detecting Mitochondrial Heteroplasmy for Clinical Diagnostics
Presented at ASHG 2017 by John Thompson, PhD and Eric White, PhD

Improved sensitivity for clinically relevant variants using orthogonal sequencing
Presented at ASHG 2016 by John Thompson, PhD

Improving coverage of poorly sequenced regions in clinical exomes
Presented at ASHG 2016 by Eric White, PhD

RIPPLY2: Believe it or not
Presented at ASHG 2016 by Natalie Vena, MS, CGC

Improved sensitivity for clinical relevant variants using orthogonal sequencing
Presented at AGBT 2016  by John Thompson, PhD

Next-Generation Sequencing test within a neurologic region of interest leads to diagnosis of RYR1-related disorder for 36-year-old female after three decades
Presented at ASHG 2015 by Pam Gerrol, M.S., CGC, Claritas Genomics and Anne Rutkowski, CMDIR

Clinical results from a pediatric neurological region of interest using an orthogonal NGS approach to identifying variants
Presented at ASHG 2015 by Eric White, Ph.D., Director, Research and Development

UPD1 in a Newborn with Multiple Congenital Anomalies
Presented at ASHG 2015 by Ann Seman, M.S., CGC

Improved Sensitivity and Rapid Confirmation of Variants via Orthogonal Sequencing of Exomes
Presented at ASHG 2015 by John Thompson, Ph.D. Chief Technology Officer

Strategies for calculating variant confidence by combining sequencing results
Presented at ASHG 2015 by Niru Chennagiri, M.S., Bioinformatics Scientist

Improving Specificity in Ion Proton Data
Presented at ASHG 2015 by Daniel Lieber, Ph.D. Assoc Director of Bioinformatics

About Claritas

Claritas Genomics serves children affected with complex genetic disorders by providing timely and accurate results, resolving families’ long search for answers. By combining clinical expertise of the world’s best pediatric specialists with innovative platform solutions, Claritas is working to improve patient care and enable new discoveries. We are committed to the highest quality and accessibility of information and our interpretive services and unique approach to reporting set the standard for reliably and clearly communicating genetic information.

Now is the time to integrate genomics into clinical practice to inform, guide and improve medical treatment for kids around the world.