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In Print: Last Week's Clinical Sequencing Papers of Note: May 8, 2013


Next generation whole genome sequencing identifies the direction of norovirus transmission in linked patients.
Kundu S, Lockwood J, Depledge DP, Chaudhry Y, et al.
Clin Infect Dis. 2013 May 3. [Epub ahead of print]

Mining exomic sequencing data to identify mutated antigens recognized by adoptively transferred tumor-reactive T cells.
Robbins PF, Lu YC, El-Gamil M, Li YF, et al.
Nat Med. 2013 May 5. [Epub ahead of print]

Population genomics of post-vaccine changes in pneumococcal epidemiology.
Croucher NJ, Finkelstein JA, Pelton SI, Mitchell PK, et al.
Nat Genet. 2013 May 5. [Epub ahead of print]

Nonsense mutation in the LGR4 gene is associated with several human diseases and other traits.
Styrkarsdottir U, Thorleifsson G, Sulem P, Gudbjartsson DF, et al.
Nature. 2013 May 5. [Epub ahead of print]

Mutations in SCO2 are associated with autosomal-dominant high-grade myopia.
Tran-Viet KN, Powell C, Barathi VA, Klemm T, et al.
Am J Hum Genet. 2013 May 2;92(5):820-6.

Mutations in DARS cause hypomyelination with brain stem and spinal cord involvement and leg spasticity.
Taft RJ, Vanderver A, Leventer RJ, Damiani SA, et al.
Am J Hum Genet. 2013 May 2;92(5):774-80.

Mutations in FGF17, IL17RD, DUSP6, SPRY4, and FLRT3 are identified in individuals with congenital hypogonadotropic hypogonadism.
Miraoui H, Dwyer AA, Sykiotis GP, Plummer L, et al.
Am J Hum Genet. 2013 May 2;92(5):725-43.

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.
Christoforides A, Carpten JD, Weiss GJ, Demeure MJ, et al.
BMC Genomics. 2013 May 4;14(1):302.

Serum microRNAs profile from genome-wide screen serves as a fingerprint for diagnosis of acute myocardial infarction and angina pectoris.
Li C, Fang Z, Jiang T, Zhang Q, et al.
BMC Med Genomics. 2013 May 4;6(1):16.

Somatic mutations in H-RAS in sporadic pheochromocytoma and paraganglioma Identified by exome sequencing.
Crona J, Delgado Verdugo A, Maharjan R, Stålberg P, et al.
J Clin Endocrinol Metab. 2013 May 2. [Epub ahead of print]

Identification of novel mutations of TP53, ALK and RET gene in metastatic thymic squamous cell carcinoma and its therapeutic implication.
Hu Z, Wang J, Yao T, Hong RL, et al.
Lung Cancer. 2013 Apr 29. [Epub ahead of print]

Molecular characterization of the fecal microbiota in patients with nonalcoholic steatohepatitis — a longitudinal study.
Wong VW, Tse CH, Lam TT, Wong GL, et al.
PLoS One. 2013 Apr 25;8(4):e62885.

Identification of novel variants in colorectal cancer families by high-throughput exome sequencing.
Derycke MS, Gunawardena SR, Middha S, Asmann YA, et al.
Cancer Epidemiol Biomarkers Prev. 2013 May 1. [Epub ahead of print]

Somatic alterations contributing to metastasis of a castration resistant prostate cancer.
Nickerson ML, Im KM, Misner KJ, Tan W, et al.
Hum Mutat. 2013 May 1. [Epub ahead of print]

Integrated genomic characterization of endometrial carcinoma.
Cancer Genome Atlas Research Network; Genome sequencing centres: Broad Institute, Getz G, Gabriel SB, Cibulskis K, Lander E, et al.
Nature. 2013 May 2;497(7447):67-73.

A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.
Kvarnung M, Nilsson D, Lindstrand A, Korenke GC, et al.
J Med Genet. 2013 May 1. [Epub ahead of print]

RNA-seq analysis of prostate cancer in the Chinese population identifies recurrent gene fusions, cancer-associated long noncoding RNAs and aberrant alternative splicings.
Ren S, Peng Z, Mao JH, Yu Y, et al.
Cell Res. 2013 May;23(5):732.

Massively parallel sequencing of maternal plasma DNA in 113 cases of fetal nuchal cystic hygroma.
Bianchi DW, Prosen T, Platt LD, Goldberg JD, et al.
Obstet Gynecol. 2013 May;121(5):1057-1062.

Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia.
The Cancer Genome Atlas Research Network.
N Engl J Med. 2013 May 1. [Epub ahead of print]

Adult-onset Alexander disease, associated with a mutation in an alternative GFAP transcript, may be phenotypically modulated by a non-neutral HDAC6 variant.
Melchionda L, Fang M, Wang H, Fugnanesi V, et al.
Orphanet J Rare Dis. 2013 May 1;8(1):66.

Ultradeep sequencing detects GNAQ and GNA11 mutations in cell-free DNA from plasma of patients with uveal melanoma.
Metz CH, Scheulen M, Bornfeld N, Lohmann D, Zeschnigk M.
Cancer Med. 2013 Apr;2(2):208-15.

A CNS-specific hypomorphic Pdgfr-beta mutant model of diabetic retinopathy.
Jadeja S, Mort RL, Keighren M, Hart AW, et al.
Invest Ophthalmol Vis Sci. 2013 Apr 30. [Epub ahead of print]

Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1.
Ramkissoon LA, Horowitz PM, Craig JM, Ramkissoon SH, et al.
Proc Natl Acad Sci U S A. 2013 Apr 30. [Epub ahead of print]

Whole-exome sequencing, without prior linkage, identifies a mutation in LAMB3 as a cause of dominant hypoplastic amelogenesis imperfecta.
Poulter JA, El-Sayed W, Shore RC, Kirkham J, et al.
Eur J Hum Genet. 2013 May 1. [Epub ahead of print]

Diagnosis of mitochondrial disorders by concomitant next-generation sequencing of the exome and mitochondrial genome.
Dinwiddie DL, Smith LD, Miller NA, Atherton AM, et al.
Genomics. 2013 Apr 27. pii: S0888-7543(13)00090-6. [Epub ahead of print]

Results of genetic testing in 855 consecutive unrelated patients referred for Long QT syndrome in a clinical laboratory.
Lieve KV, Williams L, Daly A, Richard G, et al.
Genet Test Mol Biomarkers. 2013 Apr 30. [Epub ahead of print]

CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers.
Gu F, Doderer MS, Huang YW, Roa JC, et al.
PLoS One. 2013 Apr 22;8(4):e60980.

Next-generation sequencing reveals high concordance of recurrent somatic alterations between primary tumor and metastases from patients with non-small-cell lung cancer.
Vignot S, Frampton GM, Soria JC, Yelensky R, et al.
J Clin Oncol. 2013 Apr 29. [Epub ahead of print]

RNA sequencing identifies fusion of the EWSR1 and YY1 genes in mesothelioma with t(14;22)(q32;q12).
Panagopoulos I, Thorsen J, Gorunova L, Micci F, et al.
Genes Chromosomes Cancer. 2013 Apr 30. [Epub ahead of print]

Gallbladder carcinoma: high rate of mitochondrial D-loop mutations.
Maurya SK, Tewari M, Shukla HS.
Diagn Mol Pathol. 2013 Apr 25. [Epub ahead of print]

Mitochondrial genome variations in advanced stage breast cancer: a case-control study.
Tipirisetti NR, Lakshmi RK, Govatati S, Govatati S, et al.
Mitochondrion. 2013 Apr 26. [Epub ahead of print]

EMu: probabilistic inference of mutational processes and their localization in the cancer genome.
Fischer A, Illingworth CJ, Campbell PJ, Mustonen V.
Genome Biol. 2013 Apr 29;14(4):R39.