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Last Week's Clinical Sequencing Papers of Note: Oct 5, 2011


Genetic heterogeneity of hepatitis C virus in association with antiviral therapy determined by ultra-deep sequencing.
Nasu A, Marusawa H, Ueda Y, Nishijima N, et al.
PLoS One. 2011;6(9):e24907.

Homozygosity mapping and exome sequencing reveal GATAD1 mutation in autosomal recessive dilated cardiomyopathy.
Theis JL, Sharpe KM, Matsumoto ME, Chai HS, et al.
Circ Cardiovasc Genet.2011 Sep 30. [Epub ahead of print]

Insight into the heterogeneity of breast cancer through next-generation sequencing.
Russnes HG, Navin N, Hicks J, Borresen-Dale AL.
J Clin Invest. 2011 Oct 3;121(10):3810-8.

Mutations in BRIP1 confer high risk of ovarian cancer.
Rafnar T, Gudbjartsson DF, Sulem P, Jonasdottir A, et al.
Nat Genet. 2011 Oct 2. [Epub ahead of print]

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding.
Lu R, Neff NF, Quake SR, Weissman IL.
Nat Biotechnol. 2011 Oct 2. [Epub ahead of print]

Long-range massively parallel mate pair sequencing detects distinct mutations and similar patterns of structural mutability in two breast cancer cell lines.
Hampton OA, Miller CA, Koriabine M, Li J, et al.
Cancer Genet. 2011 Aug;204(8):447-57.

Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families.
Brownstein Z, Friedman LM, Shahin H, Oron-Karni V, et al.
Genome Biol. 2011 Sep 14;12(9):R89.

Exome sequencing reveals cubilin mutation as a single-gene cause of proteinuria.
Ovunc B, Otto EA, Vega-Warner V, Saisawat P, et al.
J Am Soc Nephrol. 2011 Oct;22(10):1815-20.

Exome sequencing and subsequent association studies identify five amino acid-altering variants influencing human height.
Kim JJ, Park YM, Baik KH, Choi HY, et al.
Hum Genet. 2011 Sep 29. [Epub ahead of print]

Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity.
Kerick M, Isau M, Timmermann B, Sultmann H, et al.
BMC Med Genomics. 2011 Sep 29;4(1):68.

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Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion.
Bass AJ, Lawrence MS, Brace LE, Ramos AH, et al.
Nat Genet. 2011 Sep 4;43(10):964-8.

Toward the blood-borne miRNome of human diseases.
Keller A, Leidinger P, Bauer A, Elsharawy A, et al.
Nat Methods. 2011 Sep 4;8(10):841-3.

Hybrid selection for sequencing pathogen genomes from clinical samples.
Melnikov A, Galinsky K, Rogov P, Fennell T, et al.
Genome Biol. 2011 Aug 11;12(8):R73.

The National Institutes of Health Undiagnosed Diseases Program: Insights into rare diseases.
Gahl WA, Markello TC, Toro C, Fajardo KF, et al.
Genet Med. 2011 Sep 26. [Epub ahead of print]

Exome sequencing identifies a novel missense variant in RRM2B associated with autosomal recessive progressive external ophthalmoplegia.
Takata A, Kato M, Nakamura M, Yoshikawa T, et al.
Genome Biol. 2011 Sep 27;12(9):R92.

Evaluation of intra-host variants of the entire hepatitis B virus genome.
Ramachandran S, Zhai X, Thai H, Campo DS, et al.
PLoS One. 2011;6(9):e25232.

Performance of genotype imputation for rare variants identified in exons and flanking regions of genes.
Li L, Li Y, Browning SR, Browning BL, et al.
PLoS One. 2011;6(9):e24945.

Exome sequencing identifies a spectrum of mutation frequencies in advanced and lethal prostate cancers.
Kumar A, White TA, Mackenzie AP, Clegg N, et al.
Proc Natl Acad Sci U S A. 2011 Sep 26. [Epub ahead of print]

Exon capture analysis of G protein-coupled receptors identifies activating mutations in GRM3 in melanoma.
Prickett TD, Wei X, Cardenas-Navia I, Teer JK, et al.
Nat Genet. 2011 Sep 25. [Epub ahead of print]
(See our coverage of this paper in last week's issue here.)

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A germline variant in the TP53 polyadenylation signal confers cancer susceptibility.
Stacey SN, Sulem P, Jonasdottir A, Masson G, et al.
Nat Genet. 2011 Sep 25. [Epub ahead of print]

A simple method for the parallel deep sequencing of full influenza A genomes.
Kampmann ML, Fordyce SL, Avila-Arcos MC, Rasmussen M, et al.
J Virol Methods. 2011 Sep 17. [Epub ahead of print]

Ultra-sensitive detection of rare T cell clones.
Robins H, Desmarais C, Matthis J, Livingston R, et al.
J Immunol Methods. 2011 Sep 10. [Epub ahead of print]

Clinical pharmacogenomic testing of KRAS, BRAF and EGFR mutations by high resolution melting analysis and ultra-deep pyrosequencing.
Borras E, Jurado I, Hernan I, Gamundi MJ, et al.
BMC Cancer. 2011 Sep 24;11(1):406.

Whole-exome sequencing of DNA from peripheral blood mononuclear cells (PBMC) and EBV-transformed lymphocytes from the same donor.
Londin ER, Keller MA, D'Andrea MR, Delgrosso K, et al.
BMC Genomics. 2011 Sep 26;12(1):464.

Human immunodeficiency virus type 1 drug resistance testing: Evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit.
Stelzl E, Pröll J, Bizon B, Niklas N, et al.
J Virol Methods. 2011 Aug 27. [Epub ahead of print]

Whole-exome sequencing identifies ALMS1, IQCB1, CNGA3, and MYO7A mutations in patients with leber congenital amaurosis.
Wang X, Wang H, Cao M, Li Z, et al.
Hum Mutat. 2011 Sep 7. [Epub ahead of print]

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.