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In Print: Last Week's Clinical Sequencing Papers of Note: Jul 24, 2013


Whole-exome sequencing identifies MYO15A mutations as a cause of autosomal recessive nonsyndromic hearing loss in Korean families.
Woo HM, Park HJ, Baek JI, Park MH, et al.
BMC Med Genet. 2013 Jul 17;14(1):72.

Genomics in clinical practice: lessons from the front lines.
Jacob HJ, Abrams K, Bick DP, Brodie K, et al.
Sci Transl Med. 2013 Jul 17;5(194)

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis.
Köser CU, Bryant JM, Becq J, Török ME, et al.
N Engl J Med. 2013 Jul 18;369(3):290-2.

Mutations in DSTYK and dominant urinary tract malformations.
Sanna-Cherchi S, Sampogna RV, Papeta N, Burgess KE, Nees SN, et al.
N Engl J Med. 2013 Jul 17. [Epub ahead of print]

Towards clinical molecular diagnosis of inherited cardiac conditions: a comparison of bench-top genome DNA sequencers.
Li X, Buckton AJ, Wilkinson SL, John S, et al.
PLoS One. 2013 Jul 4;8(7):e67744.

SF3B1 mutations are associated with alternative splicing in uveal melanoma.
Furney SJ, Pedersen M, Gentien D, Dumont AG, et al.
Cancer Discov. 2013 Jul 16. [Epub ahead of print]

Whole exome sequencing identifies a causal RBM20 mutation in a large pedigree with familial dilated cardiomyopathy.
Wells QS, Becker JR, Su YR, Mosley JD, et al.
Circ Cardiovasc Genet. 2013 Jul 16. [Epub ahead of print]

Interpreting secondary cardiac disease variants in an exome cohort.
Ng D, Johnston JJ, Teer JK, Singh LN, et al.
Circ Cardiovasc Genet. 2013 Jul 16. [Epub ahead of print]

The strength of combined cytogenetic and mate-pair sequencing techniques illustrated by a germline chromothripsis rearrangement involving FOXP2.
Nazaryan L, Stefanou EG, Hansen C, Kosyakova N, et al.
Eur J Hum Genet. 2013 Jul 17. [Epub ahead of print]

Testing personalized medicine: patient and physician expectations of next-generation genomic sequencing in late-stage cancer care.
Miller FA, Hayeems RZ, Bytautas JP, Bedard PL, et al.
Eur J Hum Genet. 2013 Jul 17. [Epub ahead of print]

Autosomal recessive Adams-Oliver syndrome caused by homozygous mutation in EOGT, encoding an EGF domain-specific O-GlcNAc transferase.
Cohen I, Silberstein E, Perez Y, Landau D, et al.
Eur J Hum Genet. 2013 Jul 17. [Epub ahead of print]

Dominant form of congenital hyperinsulinism maps to HK1 region on 10q.
Pinney SE, Ganapathy K, Bradfield J, Stokes D, et al.
Horm Res Paediatr. 2013 Jul 12:18-27.

Hereditary spastic paraplegia type 43 (SPG43) is caused by mutation in C19orf12.
Landouré G, Zhu PP, Lourenço CM, Johnson JO, et al.
Hum Mutat. 2013 Jul 15. [Epub ahead of print]

Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA.
Lun FM, Chiu RW, Sun K, Leung TY, et al.
Clin Chem. 2013 Jul 15. [Epub ahead of print]

Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology.
Reuter S, Ellington MJ, Cartwright EJ, Köser CU, et al.
JAMA Intern Med. 2013 Jul 15. [Epub ahead of print]

Identification of a novel homozygous SPG7 mutation in a Japanese patient with spastic ataxia: making an efficient diagnosis using exome sequencing for autosomal recessive cerebellar ataxia and spastic paraplegia.
Doi H, Ohba C, Tsurusaki Y, Miyatake S, et al.
Intern Med. 2013;52(14):1629-33.

Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq platform.
Rutvisuttinunt W, Chinnawirotpisan P, Simasathien S, Shrestha SK, et al.
J Virol Methods. 2013 Jul 12. [Epub ahead of print]

The exomes of the NCI-60 panel: a genomic resource for cancer biology and systems pharmacology.
Abaan OD, Polley EC, Davis SR, Zhu YJ, et al.
Cancer Res. 2013 Jul 15. [Epub ahead of print]

The SAAP pipeline and database: tools to analyze the impact and predict the pathogenicity of mutations.
Al-Numair NS, Martin AC.
BMC Genomics. 2013;14 Suppl 3:S4. Epub 2013 May 28.

Identifying Mendelian disease genes with the variant effect scoring tool.
Carter H, Douville C, Stenson PD, Cooper DN, Karchin R.
BMC Genomics. 2013;14 Suppl 3:S3. Epub 2013 May 28.

Assessment of computational methods for predicting the effects of missense mutations in human cancers.
Gnad F, Baucom A, Mukhyala K, Manning G, Zhang Z.
BMC Genomics. 2013;14 Suppl 3:S7. Epub 2013 May 28.

A hypofunctional PAX1 mutation causes autosomal recessively inherited otofaciocervical syndrome.
Pohl E, Aykut A, Beleggia F, Karaca E, et al.
Hum Genet. 2013 Jul 13. [Epub ahead of print]

Biallelic nonsense mutations in the otogelin-like gene (OTOGL) in a child affected by mild to moderate hearing impairment.
Bonnet C, Louha M, Loundon N, Michalski N, et al.
Gene. 2013 Jul 10. [Epub ahead of print]

Mutations in ARL2BP, encoding ADP-ribosylation-factor-like 2 binding protein, cause autosomal-recessive retinitis pigmentosa.
Davidson AE, Schwarz N, Zelinger L, Stern-Schneider G, et al.
Am J Hum Genet. 2013 Jul 10. [Epub ahead of print]

Detection of clinically relevant genetic variants in autism spectrum disorder by whole-genome sequencing.
Jiang YH, Yuen RK, Jin X, Wang M, et al.
Am J Hum Genet. 2013 Jul 10. [Epub ahead of print]

The Scan

Suicidal Ideation-Linked Loci Identified Using Million Veteran Program Data

Researchers in PLOS Genetics identify risk variants within and across ancestry groups with a genome-wide association study involving veterans with or without a history of suicidal ideation.

Algorithm Teases Out Genetic Ancestry in Individuals at Biobank Scale

Researchers develop an algorithm known as Rye to tease apart ancestry fractions in admixed individuals at a biobank-scale, applying it to 488,221 UK Biobank participants in Nucleic Acids Research.

Multi-Ancestry Analysis Highlights Comparable Common Variants at Complex Trait-Linked Loci

Researchers in Nature Genetics examine common variants implicated in more than three dozen conditions, estimating genetic effect similarities across ancestry tracts in admixed individuals.

Sick Newborns Selected for WGS With Automated Pipeline

Researchers successfully prioritized infants with potential Mendelian conditions for whole-genome sequencing or rapid whole-genome sequencing, as they report in Genome Medicine.