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In Print: Last Week's Clinical Sequencing Papers of Note: Jun 5, 2013


Identification of driver genes in hepatocellular carcinoma by exome sequencing.
Cleary SP, Jeck WR, Zhao X, Kuichen, et al.
Hepatology. 2013 May 31. [Epub ahead of print]

Views of genetics health professionals on the return of genomic results.
Grove ME, Wolpert MN, Cho MK, Lee SS, Ormond KE.
J Genet Couns. 2013 Jun 2. [Epub ahead of print]

Parkinsonism and distinct dementia patterns in a family with the MAPT R406W mutation.
Carney RM, Kohli MA, Kunkle BW, Naj AC, et al.
Alzheimers Dement. 2013 May 30. [Epub ahead of print]

A homozygous mucosa-associated lymphoid tissue 1 (MALT1) mutation in a family with combined immunodeficiency.
Jabara HH, Ohsumi T, Chou J, Massaad MJ, et al.
J Allergy Clin Immunol. 2013 May 30. [Epub ahead of print]

Using next-generation sequencing as a genetic diagnostic tool in rare autosomal recessive neurologic Mendelian disorders.
Chen Z, Wang JL, Tang BS, Sun ZF, et al.
Neurobiol Aging. 2013 May 30. [Epub ahead of print]

A novel missense mutation of FGFR3 in a Chinese female and her fetus with hypochondroplasia by next-generation sequencing.
Wang H, Sun Y, Wu W, Wei X, et al.
Clin Chim Acta. 2013 Aug 23;423C:62-65.

The first case of CDK5RAP2-related primary microcephaly in a non-consanguineous patient identified by next generation sequencing.
Tan CA, Topper S, Ward Melver C, Stein J, et al.
Brain Dev. 2013 May 28. [Epub ahead of print]

Next generation sequencing in psychiatric research: what study participants need to know about research findings.
Mathieu G, Groisman IJ, Godard B.
Int J Neuropsychopharmacol. 2013 Jun 3:1-9. [Epub ahead of print]

A novel APOB mutation identified by exome sequencing cosegregates with steatosis, liver cancer, and hypocholesterolemia.
Cefalù AB, Pirruccello JP, Noto D, Gabriel S, et al.
Arterioscler Thromb Vasc Biol. 2013 May 30. [Epub ahead of print]

Return of incidental findings in genomic medicine: measuring what patients value-development of an instrument to measure preferences for information from next-generation testing (IMPRINT).
Bennette CS, Trinidad SB, Fullerton SM, Patrick D, et al.
Genet Med. 2013 May 30. [Epub ahead of print]

Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumonia isolates using whole genomic sequence data.
Stoesser N, Batty EM, Eyre DW, Morgan M, et al.
J Antimicrob Chemother. 2013 May 30. [Epub ahead of print]

HUWE1 mutation explains phenotypic severity in a case of familial idiopathic intellectual disability.
Isrie M, Kalscheuer VM, Holvoet M, Fieremans N, et al.
Eur J Med Genet. 2013 May 27. [Epub ahead of print]

Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology.
Chen C, Zhang W, Zheng H, Lan R, et al.
J Clin Microbiol. 2013 May 29. [Epub ahead of print]

Replication fitness of multiple NNRTI-resistant HIV-1 variants in the presence of etravirine measured by 454 deep sequencing.
Brumme CJ, Huber KD, Dong W, Poon AF, et al.
J Virol. 2013 May 29. [Epub ahead of print]

Gut metagenome in European women with normal, impaired and diabetic glucose control.
Karlsson FH, Tremaroli V, Nookaew I, Bergström G, et al.
Nature. 2013 May 29. [Epub ahead of print]

The new genetics and informed consent: differentiating choice to preserve autonomy.
Bunnik EM, de Jong A, Nijsingh N, de Wert GM.
Bioethics. 2013 May 30. [Epub ahead of print]

Target enrichment and high-throughput sequencing of 80 ribosomal protein genes to identify mutations associated with Diamond-Blackfan anaemia.
Gerrard G, Valgañón M, Foong HE, Kasperaviciute D, et al.
Br J Haematol. 2013 May 30. [Epub ahead of print]

Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing.
Xu B, Zhi N, Hu G, Wan Z, et al.
Proc Natl Acad Sci U S A. 2013 May 28. [Epub ahead of print]

ZNF408 is mutated in familial exudative vitreoretinopathy and is crucial for the development of zebrafish retinal vasculature.
Collin RW, Nikopoulos K, Dona M, Gilissen C, et al.
Proc Natl Acad Sci U S A. 2013 May 28. [Epub ahead of print]

Homozygous mutations in a predicted endonuclease cause congenital dyserythropoietic anemia type I.
Babbs C, Roberts NA, Sanchez-Pulido L, McGowan SJ, et al.
Haematologica. 2013 May 28. [Epub ahead of print]

Next-generation-sequencing-spectratyping reveals public T-cell receptor repertoires in pediatric very severe aplastic anemia and identifies a beta chain CDR3 sequence associated with hepatitis-induced pathogenesis.
Krell PF, Reuther S, Fischer U, Keller T, et al.
Haematologica. 2013 May 28. [Epub ahead of print]

Cell-type, allelic and genetic signatures in the human pancreatic beta cell transcriptome.
Nica AC, Ongen H, Irminger JC, Bosco D, et al.
Genome Res. 2013 May 28. [Epub ahead of print]

Developmental dysplasia of the hip: Linkage mapping and whole exome sequencing identify a shared variant in CX3CR1 in all affected members of a large multi-generation family.
Feldman GJ, Parvizi J, Levenstien M, Scott K, et al.
J Bone Miner Res. 2013 May 29. [Epub ahead of print]

Genome-wide identification of genes with amplification and/or fusion in small cell lung cancer.
Iwakawa R, Takenaka M, Kohno T, Shimada Y, et al.
Genes Chromosomes Cancer. 2013 May 28. [Epub ahead of print]

Diversity of the vaginal microbiome correlates with preterm birth.
Hyman RW, Fukushima M, Jiang H, Fung E, et al.
Reprod Sci. 2013 May 28. [Epub ahead of print]

Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas.
Palles C, Cazier JB, Howarth KM, Domingo E, et al.
Nat Genet. 2013 May 29;45(6):713.

Multiple variants aggregate in the neuregulin signaling pathway in a subset of schizophrenia patients.
Hatzimanolis A, McGrath JA, Wang R, Li T, et al.
Transl Psychiatry. 2013 May 28;3:e264.

Novel form of X-linked nonsyndromic hearing loss with cochlear malformation caused by a mutation in the type IV collagen gene COL4A6.
Rost S, Bach E, Neuner C, Nanda I, et al.
Eur J Hum Genet. 2013 May 29. [Epub ahead of print]

Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline.
Hadj Khodabakhshi A, Fejes AP, Birol I, Jones SJ.
BMC Bioinformatics. 2013 May 28;14(1):167.

Ethical and legal implications of whole genome and whole exome sequencing in African populations.
Wright GE, Koornhof PG, Adeyemo AA, Tiffin N.
BMC Med Ethics. 2013 May 28;14(1):21.

Molecular epidemiology of community-associated methicillin-resistant Staphylococcus aureus in the genomic era: a cross-sectional study.
Prosperi M, Veras N, Azarian T, Rathore M, et al.
Sci Rep. 2013 May 28;3:1902.

Mutascope: sensitive detection of somatic mutations from deep amplicon sequencing.
Yost SE, Alakus H, Matsui H, Schwab RB, et al.
Bioinformatics. 2013 May 27. [Epub ahead of print]