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In Print: Clinical Sequencing Papers of Note from the Last Two Weeks

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Exome sequencing reveals a novel PRPS1 mutation in a family with CMTX5 without optic atrophy.
Park J, Hyun YS, Kim YJ, Nam SH, et al.
J Clin Neurol. 2013 Oct;9(4):283-288.


Ciliary Genes TBC1D32/C6orf170 and SCLT1 are Mutated in Patients with OFD Type IX.
Adly N, Alhashem A, Ammari A, Alkuraya FS.
Hum Mutat. 2013 Nov 6. [Epub ahead of print]


Enhanced Sensitivity for Detection of Low-level Germline Mosaic RB1 Mutations in Sporadic Retinoblastoma Cases Using Deep Semi-conductor Sequencing.
Chen Z, Moran K, Richards-Yutz J, Toorens E, et al.
Hum Mutat. 2013 Nov 26. [Epub ahead of print]


Quantifying rare, deleterious variation in 12 human Cytochrome P450 drug-metabolism genes in a large-scale exome dataset.
Gordon AS, Tabor HK, Johnson AD, Snively BM, et al.
Hum Mol Genet. 2013 Nov 26. [Epub ahead of print]


Research participants' attitudes towards the confidentiality of genomic sequence information.
Jamal L, Sapp JC, Lewis K, Yanes T, et al.
Eur J Hum Genet. 2013 Nov 27. [Epub ahead of print]


Deleterious mutation in FDX1L gene is associated with a novel mitochondrial muscle myopathy.
Spiegel R, Saada A, Halvardson J, Soiferman D, et al.
Eur J Hum Genet. 2013 Nov 27. [Epub ahead of print]


Exome sequencing in developmental eye disease leads to identification of causal variants in GJA8, CRYGC, PAX6 and CYP1B1.
Prokudin I, Simons C, Grigg JR, Storen R, et al.
Eur J Hum Genet. 2013 Nov 27. [Epub ahead of print]


Exome Sequencing Finds a Novel PCSK1 Mutation in a Child With Generalized Malabsorptive Diarrhea and Diabetes Insipidus.
Yourshaw M, Solorzano-Vargas RS, Pickett LA, Lindberg I, et al.
J Pediatr Gastroenterol Nutr. 2013 Dec;57(6):759-67.


Impact of next generation sequencing on diagnostics in a genetic skin disease clinic.
Takeichi T, Nanda A, Liu L, Salam A, et al.
Exp Dermatol. 2013 Dec;22(12):825-31.


Quantitative Identification of Mutant Alleles Derived from Lung Cancer in Plasma Cell-Free DNA via Anomaly Detection Using Deep Sequencing Data.
Kukita Y, Uchida J, Oba S, Nishino K, et al.
PLoS One. 2013 Nov 21;8(11):e81468.


ADCK4 mutations promote steroid-resistant nephrotic syndrome through CoQ10 biosynthesis disruption.
Ashraf S, Gee HY, Woerner S, Xie LX, et al.
J Clin Invest. 2013 Nov 25. [Epub ahead of print]


Exome sequencing identifies CTSK mutations in patients originally diagnosed as intermediate osteopetrosis.
Pangrazio A, Puddu A, Oppo M, Valentini M, et al.
Bone. 2013 Nov 20. [Epub ahead of print]


Mutations in FAM111B Cause Hereditary Fibrosing Poikiloderma with Tendon Contracture, Myopathy, and Pulmonary Fibrosis.
Mercier S, Küry S, Shaboodien G, Houniet DT, et al.
Am J Hum Genet. 2013 Nov 19. [Epub ahead of print]


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, et al.
Am J Hum Genet. 2013 Nov 19. [Epub ahead of print]


Joint Linkage and Association Analysis with Exome Sequence Data Implicates SLC25A40 in Hypertriglyceridemia.
Rosenthal EA, Ranchalis J, Crosslin DR, Burt A, et al.
Am J Hum Genet. 2013 Nov 19. [Epub ahead of print]


Mutations in Endothelin 1 Cause Recessive Auriculocondylar Syndrome and Dominant Isolated Question-Mark Ears.
Gordon CT, Petit F, Kroisel PM, Jakobsen L, et al.
Am J Hum Genet. 2013 Nov 19. [Epub ahead of print]


Comprehensive Analysis of Long Non-Coding RNAs in Ovarian Cancer Reveals Global Patterns and Targeted DNA Amplification.
Akrami R, Jacobsen A, Hoell J, Schultz N, et al.
PLoS One. 2013 Nov 12;8(11):e80306.


Increasing the Yield in Targeted Next-Generation Sequencing by Implicating CNV Analysis, Non-Coding Exons and the Overall Variant Load: The Example of Retinal Dystrophies.
Eisenberger T, Neuhaus C, Khan AO, Decker C, et al.
PLoS One. 2013 Nov 12;8(11):e78496.


SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data.
Chen M, Gunel M, Zhao H.
PLoS One. 2013 Nov 12;8(11):e78143.


Clinical characteristics of early retinal disease due to CDHR1 mutation.
Ba-Abbad R, Sergouniotis PI, Plagnol V, Robson AG, et al.
Mol Vis. 2013 Nov 16;19:2250-2259.


Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia.
Ferreira PG, Jares P, Rico D, Gómez-López G, et al.
Genome Res. 2013 Nov 21. [Epub ahead of print]


MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition.
Wagle N, Van Allen EM, Treacy DJ, Frederick DT, et al.
Cancer Discov. 2013 Nov 21. [Epub ahead of print]


The Genetic Landscape of Clinical Resistance to RAF Inhibition in Metastatic Melanoma.
Van Allen EM, Wagle N, Sucker A, Treacy DJ, et al.
Cancer Discov. 2013 Nov 21. [Epub ahead of print]


Identification of Novel Long Noncoding RNAs Associated with TGF-β/Smad3-Mediated Renal Inflammation and Fibrosis by RNA Sequencing.
Zhou Q, Chung AC, Huang XR, Dong Y, et al.
Am J Pathol. 2013 Nov 18. [Epub ahead of print]


Exploration of the gene fusion landscape of glioblastoma using transcriptome sequencing and copy number data.
Shah N, Lankerovich M, Lee H, Yoon JG, et al.
BMC Genomics. 2013 Nov 22;14(1):818.


SNP Linkage Analysis and Whole Exome Sequencing Identify a Novel POU4F3 Mutation in Autosomal Dominant Late-Onset Nonsyndromic Hearing Loss (DFNA15).
Kim HJ, Won HH, Park KJ, Hong SH, et al.
PLoS One. 2013 Nov 18;8(11):e79063.


Emergence of the Virulence-associated PB2 E627K Substitution in a Fatal Human Case of Highly Pathogenic Avian Influenza Virus A(H7N7) Infection Determined by Illumina Ultra-deep Sequencing.
Jonges M, Welkers MR, Jeeninga RE, Meijer A, et al.
J Virol. 2013 Nov 20. [Epub ahead of print]


Identification and Characterization of Functional Risk Variants for Colorectal Cancer Mapping to Chromosome 11q23.1.
Biancolella M, Fortini BK, Tring S, Plummer SJ, et al.
Hum Mol Genet. 2013 Nov 20. [Epub ahead of print]


Characterization of RNA in exosomes secreted by human breast cancer cell lines using next-generation sequencing.
Jenjaroenpun P, Kremenska Y, Nair VM, Kremenskoy M, et al.
PeerJ. 2013 Nov 5;1:e201.


Treatable childhood neuronopathy caused by mutations in riboflavin transporter RFVT2.
Foley AR, Menezes MP, Pandraud A, Gonzalez MA, et al.
Brain. 2013 Nov 19. [Epub ahead of print]


Detection of mitochondrial DNA mutations by high-throughput sequencing in the blood of breast cancer patients.
Li LH, Kang T, Chen L, Zhang W, et al.
Int J Mol Med. 2013 Nov 19. [Epub ahead of print]


A Novel GBA2 Gene Missense Mutation in Spastic Ataxia.
Votsi C, Zamba-Papanicolaou E, Middleton LT, Pantzaris M, Christodoulou K.
Ann Hum Genet. 2013 Nov 20. [Epub ahead of print]


Somatic point mutation calling in low cellularity tumors.
Kassahn KS, Holmes O, Nones K, Patch AM, et al.
PLoS One. 2013 Nov 8;8(11):e74380.


Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases.
Satoh J, Kawana N, Yamamoto Y.
Gene Regul Syst Bio. 2013 Nov 4;7:139-52.


Cell-Free DNA Analysis for Trisomy Risk Assessment in First-Trimester Twin Pregnancies.
Gil MD, Quezada MS, Bregant B, Syngelaki A, Nicolaides KH.
Fetal Diagn Ther. 2013 Nov 15. [Epub ahead of print]


Rare Variants in PLXNA4 and Parkinson's Disease.
Schulte EC, Stahl I, Czamara D, Ellwanger DC, et al.
PLoS One. 2013 Nov 11;8(11):e79145.


An integrated inspection of the somatic mutations in a lung squamous cell carcinoma using next-generation sequencing.
Stead LF, Egan P, Devery A, Conway C, et al.
PLoS One. 2013 Nov 11;8(11):e78823.


Recurrent Tissue-Specific mtDNA Mutations Are Common in Humans.
Samuels DC, Li C, Li B, Song Z, et al.
PLoS Genet. 2013 Nov;9(11):e1003929.


Power of Family-Based Association Designs to Detect Rare Variants in Large Pedigrees Using Imputed Genotypes.
Saad M, Wijsman EM.
Genet Epidemiol. 2013 Nov 15. [Epub ahead of print]


Full-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one.
Dudley DM, Karl JA, Creager HM, Bohn PS, et al.
Immunogenetics. 2013 Nov 16. [Epub ahead of print]


Gain-of-function mutations in the phosphatidylserine synthase 1 (PTDSS1) gene cause Lenz-Majewski syndrome.
Sousa SB, Jenkins D, Chanudet E, Tasseva G, et al.
Nat Genet. 2013 Nov 17. [Epub ahead of print]


Rare variants in LRRK1 and Parkinson's disease.
Schulte EC, Ellwanger DC, Dihanich S, Manzoni C, et al.
Neurogenetics. 2013 Nov 16. [Epub ahead of print]


Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis.
Kim HP, Cho GA, Han SW, Shin JY, et al.
Oncogene. 2013 Nov 18. [Epub ahead of print]


Targeted sequencing in candidate genes for atrial fibrillation: the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Targeted Sequencing Study.
Lin H, Sinner MF, Brody JA, Arking DE, et al.
Heart Rhythm. 2013 Nov 14. [Epub ahead of print]


Family-based exome-sequencing approach identifies rare susceptibility variants for lithium-responsive bipolar disorder.
Cruceanu C, Ambalavanan A, Spiegelman D, Gauthier J, et al.
Genome. 2013 Oct;56(10):634-40.


The Cancer Genome Atlas Pan-Cancer analysis project.
Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, Mills GB, Shaw KR, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM.
Nat Genet. 2013 Oct;45(10):1113-20.

The Scan

Omicron's Emergence

The World Health Organization has called Omicron a SARS-CoV-2 "variant of concern," the Los Angeles Times writes.

Not as Much

Merck's pill to treat COVID-19 reduces the risk of hospitalization and death among COVID-19 patients by less than previously reported, the New York Times says.

Bats That Hang Together

Discover magazine writes that researchers have found a social microbiome among vampire bats.

PLOS Papers on CEWAS, Simian Varicella Virus Transcriptome, Dermatomyositis Markers

In PLOS this week: multi-omic approach to home in on genetic risk variants, transcriptomic analysis of the simian varicella virus, and more.