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In Print: Last Week's Clinical Sequencing Papers of Note: Jan 16, 2013


A deletion mutation in TMEM38B associated with autosomal recessive osteogenesis imperfecta.
Volodarsky M, Markus B, Cohen I, Staretz-Chacham O, et al.
Hum Mutat. 2013 Jan 12. [Epub ahead of print]

Non optical massive parallel DNA sequencing of BRCA1 and BRCA2 genes in a diagnostic setting.
Costa JL, Sousa S, Justino A, Kay T, et al.
Hum Mutat. 2013 Jan 11. [Epub ahead of print]

Breakpoint mapping by next generation sequencing reveals causative gene disruption in patients carrying apparently balanced chromosome rearrangements with intellectual deficiency and/or congenital malformations.
Schluth-Bolard C, Labalme A, Cordier MP, Till M, et al.
J Med Genet. 2013 Jan 12. [Epub ahead of print]

Heterogeneity of mutational mechanisms and modes of inheritance in auriculocondylar syndrome.
Gordon CT, Vuillot A, Marlin S, Gerkes E, et al.
J Med Genet. 2013 Jan 12. [Epub ahead of print]

Whole-exome sequencing identifies a mutation in the mitochondrial ribosome protein MRPL44 to underlie mitochondrial infantile cardiomyopathy.
Carroll CJ, Isohanni P, Pöyhönen R, Euro L, et al.
J Med Genet. 2013 Jan 12. [Epub ahead of print]

Successful noninvasive trisomy 18 detection using single molecule sequencing.
van den Oever JM, Balkassmi S, Johansson LF, Adama van Scheltema PN, et al.
Clin Chem. 2013 Jan 11. [Epub ahead of print]

Resequencing and clinical associations of the 9p21.3 region: a comprehensive investigation in the Framingham heart study.
Johnson AD, Hwang SJ, Voorman A, Morrison A, et al.
Circulation. 2013 Jan 11. [Epub ahead of print]

Exome sequencing identified NRG3 as a novel susceptible gene of Hirschsprung's disease in a Chinese population.
Yang J, Duan S, Zhong R, Yin J, et al.
Mol Neurobiol. 2013 Jan 12. [Epub ahead of print]

Transcriptome sequencing (RNA-Seq) of human endobronchial biopsies: asthma versus controls.
Yick CY, Zwinderman AH, Kunst PW, Grünberg K, et al.
Eur Respir J. 2013 Jan 11. [Epub ahead of print]

Whole-exome sequencing identifies a recurrent NAB2-STAT6 fusion in solitary fibrous tumors.
Chmielecki J, Crago AM, Rosenberg M, O'Connor R, et al.
Nat Genet. 2013 Jan 13. [Epub ahead of print]

Identification of recurrent NAB2-STAT6 gene fusions in solitary fibrous tumor by integrative sequencing.
Robinson DR, Wu YM, Kalyana-Sundaram S, Cao X, et al.
Nat Genet. 2013 Jan 13. [Epub ahead of print]

Noninvasive detection of fetal subchromosome abnormalities via deep sequencing of maternal plasma.
Srinivasan A, Bianchi DW, Huang H, Sehnert AJ, Rava RP.
Am J Hum Genet. 2013 Jan 9. [Epub ahead of print]

ALDH1A3 mutations cause recessive anophthalmia and microphthalmia.
Fares-Taie L, Gerber S, Chassaing N, Clayton-Smith J, et al.
Am J Hum Genet. 2013 Jan 9. [Epub ahead of print]

Evaluation of targeted next-generation sequencing-based preimplantation genetic diagnosis of monogenic disease.
Treff NR, Fedick A, Tao X, Devkota B, et al.
Fertil Steril. 2013 Jan 9. [Epub ahead of print]

Base-pair-resolution DNA methylome of the EBV-positive endemic Burkitt lymphoma cell line DAUDI determined by SOLiD bisulfite-sequencing.
Kreck B, Richter J, Ammerpohl O, Barann M, et al.
Leukemia. 2013 Jan 11. [Epub ahead of print]

A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak.
Reuter S, Harrison TG, Köser CU, Ellington MJ, et al.
BMJ Open. 2013 Jan 9;3(1).

RNA-seq analysis of the parietal cortex in Alzheimer's disease reveals alternatively spliced isoforms related to lipid metabolism.
Mills JD, Nalpathamkalam T, Jacobs HI, Janitz C, et al.
Neurosci Lett. 2013 Jan 7. [Epub ahead of print]

Low-abundance resistant mutations in HIV-1 subtype C antiretroviral therapy-naïve individuals as revealed by pyrosequencing.
Gonzalez S, Tully DC, Gondwe C, Wood C.
Curr HIV Res. 2013 Jan 11. [Epub ahead of print]

A pilot study comparing HPV-positive and HPV-negative head and neck squamous cell carcinomas by whole exome sequencing.
Nichols AC, Chan-Seng-Yue M, Yoo J, Xu W, et al.
ISRN Oncol. 2012;2012:809370.

Evaluation of DNA from the papanicolaou test to detect ovarian and endometrial cancers.
Kinde I, Bettegowda C, Wang Y, Wu J, et al.
Sci Transl Med. 2013 Jan 9;5(167):167ra4.

RNA-seq analysis implicates dysregulation of the immune system in schizophrenia.
Xu J, Sun J, Chen J, Wang L, et al.
BMC Genomics. 2012;13 Suppl 8:S2.

Reconstructing genome mixtures from partial adjacencies.
Mahmoody A, Kahn CL, Raphael BJ.
BMC Bioinformatics. 2012;13 Suppl 19:S9.

Comprehensive analysis of microRNAs in breast cancer.
Chang HT, Li SC, Ho MR, Pan HW, et al.
BMC Genomics. 2012;13 Suppl 7:S18.

RNA-seq profiling of spinal cord motor neurons from a presymptomatic SOD1 ALS mouse.
Bandyopadhyay U, Cotney J, Nagy M, Oh S, et al.
PLoS One. 2013;8(1):e53575.

Exome capture sequencing of adenoma reveals genetic alterations in multiple cellular pathways at the early stage of colorectal tumorigenesis.
Zhou D, Yang L, Zheng L, Ge W, et al.
PLoS One. 2013;8(1):e53310.

Duplication of C7orf58, WNT16 and FAM3C in an obese female with a t(7;22)(q32.1;q11.2) chromosomal translocation and clinical features resembling Coffin-Siris syndrome.
Zhu J, Qiu J, Magrane G, Abedalthagafi M, et al.
PLoS One. 2012;7(12):e52353.

ELF5 suppresses estrogen sensitivity and underpins the acquisition of antiestrogen resistance in luminal breast cancer.
Kalyuga M, Gallego-Ortega D, Lee HJ, Roden DL, et al.
PLoS Biol. 2012 Dec;10(12):e1001461.

Patient-specific induced pluripotent stem cells derived cardiomycoytes recapitulates the pathogenic phenotypes of dilated cardiomyopathy due to a novel DES mutation identified by whole Exome sequencing.
Tse HF, Ho JC, Choi SW, Lee YK, et al.
Hum Mol Genet. 2013 Jan 8. [Epub ahead of print]

IgG4+ clones identified by next-generation sequencing dominate the b-cell receptor repertoire in IgG4-associated cholangitis.
de Buy Wenniger LJ, Doorenspleet ME, Klarenbeek PL, Verheij J, et al.
Hepatology. 2013 Jan 8. [Epub ahead of print]

A genomic portrait of the emergence, evolution and global spread of a methicillin resistant Staphylococcus aureus pandemic.
Holden MT, Hsu LY, Kurt K, Weinert LA, et al.
Genome Res. 2013 Jan 8. [Epub ahead of print]

New population-based exome data are questioning the pathogenicity of previously cardiomyopathy-associated genetic variants.
Andreasen C, Nielsen JB, Refsgaard L, Holst AG, et al.
Eur J Hum Genet. 2013 Jan 9. [Epub ahead of print]

Non-invasive prenatal testing of fetal whole chromosome aneuploidy by massively parallel sequencing.
Liang D, Lv W, Wang H, Xu L, et al.
Prenat Diagn. 2013 Jan 9. [Epub ahead of print]

The tumorigenic FGFR3-TACC3 gene fusion escapes miR-99a regulation in glioblastoma.
Parker BC, Annala MJ, Cogdell DE, Granberg KJ, et al.
J Clin Invest. 2013 Jan 9. pii: 67144.

A new locus for X-linked dominant Charcot Marie Tooth disease (CMTX6) is caused by mutations in the pyruvate dehydrogenase kinase isoenzyme 3 (PDK3) gene.
Kennerson ML, Yiu EM, Chuang DT, Kidambi A, et al.
Hum Mol Genet. 2013 Jan 7. [Epub ahead of print]

Cathepsin F mutations cause Type B Kufs disease, an adult-onset neuronal ceroid lipofuscinosis.
Smith KR, Dahl HH, Canafoglia L, Andermann E, et al.
Hum Mol Genet. 2013 Jan 7. [Epub ahead of print]

Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma.
Green MR, Gentles AJ, Nair RV, Irish JM, et al.
Blood. 2013 Jan 7. [Epub ahead of print]

Severe combined immunodeficiency resulting from mutations in MTHFD1.
Keller MD, Ganesh J, Heltzer M, Paessler M, et al.
Pediatrics. 2013 Jan 6. [Epub ahead of print]

Rapid gene identification in a Chinese osteopetrosis family by whole exome sequencing.
Sui W, Ou M, Liang J, Ding M, et al.
Gene. 2013 Jan 4. pii: S0378-1119(12)01631-9.

A resequence analysis of genomic loci on chromosomes 1q32.1, 5p15.33, and 13q22.1 associated with pancreatic cancer risk.
Parikh H, Jia J, Zhang X, Chung CC, et al.
Pancreas. 2013 Jan 3. [Epub ahead of print]

Unique genome-wide map of TCF4 and STAT3 targets using ChIP-seq reveals their association with new molecular subtypes of glioblastoma.
Zhang JX, Zhang J, Yan W, Wang YY, et al.
Neuro Oncol. 2013 Jan 7. [Epub ahead of print]