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In Print: Last Week's Clinical Sequencing Papers of Note: Apr 4, 2012


Comprehensive resequence analysis of a 123-kb region of chromosome 11q13 associated with prostate cancer.
Chung CC, Boland J, Yeager M, Jacobs KB, et al.
Prostate. 2012 Apr;72(5):476-86.

Joint rare variant association test of the average and individual effects for sequencing studies.
Wang Y, Chen YH, Yang Q.
PLoS One. 2012;7(3):e32485.

Rapid detection of the ACMG/ACOG-recommended 23 CFTR disease-causing mutations using Ion Torrent semiconductor sequencing.
Elliott AM, Radecki J, Moghis B, Li X, Kammesheidt A.
J Biomol Tech. 2012 Apr;23(1):24-30.

Random amplification and pyrosequencing for identification of novel viral genome sequences.
Hang J, Forshey BM, Kochel TJ, Li T, et al.
J Biomol Tech. 2012 Apr;23(1):4-10.

Comprehensive DNA copy number profile and BAC library construction of an Indian individual.
Chakrabarty S, D'Souza RR, Bellampalli R, Rotti H, et al.
Gene. 2012 Mar 21. [Epub ahead of print]

Exome sequencing identifies PDE4D mutations in acrodysostosis.
Lee H, Graham JM Jr, Rimoin DL, Lachman RS, et al.
Am J Hum Genet. 2012 Mar 28. [Epub ahead of print]

Rare mutations in XRCC2 increase the risk of breast cancer.
Park DJ, Lesueur F, Nguyen-Dumont T, Pertesi M, et al.
Am J Hum Genet. 2012 Mar 28. [Epub ahead of print]

Exome sequencing identifies PDE4D mutations as another cause of acrodysostosis.
Michot C, Le Goff C, Goldenberg A, Abhyankar A, et al.
Am J Hum Genet. 2012 Mar 28. [Epub ahead of print]

Chromosome-selective sequencing of maternal plasma cell-free DNA for first-trimester detection of trisomy 21 and trisomy 18.
Ashoor G, Syngelaki A, Wagner M, Birdir C, Nicolaides KH.
Am J Obstet Gynecol. 2012 Apr;206(4):322.e1-5.

Ion Torrent PGM sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.
Vogel U, Szczepanowski R, Claus H, Jünemann S, et al.
J Clin Microbiol. 2012 Mar 29. [Epub ahead of print]

Exome sequencing reveals a pallidin mutation in a Hermansky-Pudlak-like primary immunodeficiency syndrome.
Badolato R, Prandini A, Caracciolo S, Colombo F, et al.
Blood. 2012 Mar 29;119(13):3185-7.

Systematic analysis and functional annotation of variations in the genome of an Indian individual.
Patowary A, Purkanti R, Singh M, Chauhan RK, et al.
Hum Mutat. 2012 Mar 27. [Epub ahead of print]

Targeted exome sequencing in clear cell renal cell carcinoma tumors suggests aberrant chromatin regulation as a crucial step in ccRCC development.
Duns G, Hofstra RM, Sietzema JG, Hollema H, et al.
Hum Mutat. 2012 Mar 27. [Epub ahead of print]

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
Barretina J, Caponigro G, Stransky N, Venkatesan K, et al.
Nature. 2012 Mar 28;483(7391):603-7.

Two-phase stratified sampling designs for regional sequencing.
Chen Z, Craiu RV, Bull SB.
Genet Epidemiol. 2012 Mar 28. [Epub ahead of print]

Accurate imputation of rare and common variants in a founder population from a small number of sequenced individuals.
Uricchio LH, Chong JX, Ross KD, Ober C, Nicolae DL.
Genet Epidemiol. 2012 Mar 28. [Epub ahead of print]

Tailored enrichment strategy detects low abundant small noncoding RNAs in HIV-1 infected cells.
Althaus CF, Vongrad V, Niederost B, Joos B, et al.
Retrovirology. 2012 Mar 29;9(1):27.

Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: coccidia differing in host range and transmission strategy.
Reid AJ, Vermont SJ, Cotton JA, Harris D, et al.
PLoS Pathog. 2012 Mar;8(3):e1002567.

Deep sequencing reveals minor protease resistance mutants in patients failing a protease inhibitor regimen.
Fisher R, van Zyl GU, Travers SA, Kosakovsky Pond SL, et al.
J Virol. 2012 Mar 28. [Epub ahead of print]

Next-generation sequencing demands next-generation phenotyping.
Hennekam RC, Biesecker LG.
Hum Mutat. 2012 Feb 13. [Epub ahead of print]

Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations.
O'Roak BJ, Deriziotis P, Lee C, Vives L, et al.
Nat Genet. 2012 Mar 28;44(4):471.

Fatal neonatal lactic acidosis due to a novel de novo mitochondrial G7453A tRNA-Serine ((UCN)) mutation.
Götz A, Isohanni P, Liljeström B, Rummukainen J, et al.
Pediatr Res. 2012 Mar 27. [Epub ahead of print]

The changing landscape of genetic testing and its impact on clinical and laboratory services and research in Europe.
Hastings R, de Wert G, Fowler B, Krawczak M, et al.
Eur J Hum Genet. 2012 Mar 28. [Epub ahead of print]

MAX mutations cause hereditary and sporadic pheochromocytoma and paraganglioma.
Burnichon N, Cascon A, Schiavi F, Paes Morales N, et al.
Clin Cancer Res. 2012 Mar 27. [Epub ahead of print]

RNA-seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts.
Driver AM, Penagaricano F, Huang W, Ahmad KR, et al.
BMC Genomics. 2012 Mar 28;13(1):118.

Insights into Chinese prostate cancer with RNA-seq.
Sahu A, Iyer MK, Chinnaiyan AM.
Cell Res. 2012 Mar 27. [Epub ahead of print]

Decade-long bacterial community dynamics in cystic fibrosis airways.
Zhao J, Schloss PD, Kalikin LM, Carmody LA, et al.
Proc Natl Acad Sci U S A. 2012 Mar 26. [Epub ahead of print]

Transcriptome landscape of the human placenta.
Kim J, Zhao K, Jiang P, Lu ZX, et al.
BMC Genomics. 2012 Mar 27;13(1):115.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.