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In Print: Last Week's Clinical Sequencing Papers of Note: Feb 6, 2013


Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL.
Tzoneva G, Perez-Garcia A, Carpenter Z, Khiabanian H, et al.
Nat Med. 2013 Feb 3. [Epub ahead of print]

Relapse-specific mutations in NT5C2 in childhood acute lymphoblastic leukemia.
Meyer JA, Wang J, Hogan LE, Yang JJ, et al.
Nat Genet. 2013 Feb 3. [Epub ahead of print]

Loss-of-function mutations in SMARCE1 cause an inherited disorder of multiple spinal meningiomas.
Smith MJ, O'Sullivan J, Bhaskar SS, Hadfield KD, et al.
Nat Genet. 2013 Feb 3. [Epub ahead of print]

Deep sequencing of small RNA transcriptome reveals novel non-coding RNAs in hepatocellular carcinoma.
Law PT, Qin H, Ching AK, Lai KP, et al.
J Hepatol. 2013 Jan 29. [Epub ahead of print]

Discovery of novel non-synonymous SNP variants in 988 candidate genes from 6 centenarians by target capture and next-generation sequencing.
Han J, Ryu S, Moskowitz DM, Rothenberg D, et al.
Mech Ageing Dev. 2013 Jan 31. [Epub ahead of print]

Exome sequencing reveals a homozygous mutation in TWINKLE as the cause of multisystemic failure including renal tubulopathy in three siblings.
Prasad C, Melançon SB, Rupar CA, Prasad AN, et al.
Mol Genet Metab. 2012 Dec 31. [Epub ahead of print]

Identification of mutations in SLC24A4, encoding a potassium-dependent sodium/calcium exchanger, as a cause of amelogenesis imperfecta.
Parry DA, Poulter JA, Logan CV, Brookes SJ, et al.
Am J Hum Genet. 2013 Jan 29. [Epub ahead of print]

Juvenile cataract morphology in 3 siblings not yet diagnosed with cerebrotendinous xanthomatosis.
Khan AO, Aldahmesh MA, Mohamed JY, Alkuraya FS.
Ophthalmology. 2013 Jan 30. [Epub ahead of print]

Bacterial diversity in two neonatal intensive care units (NICUs).
Hewitt KM, Mannino FL, Gonzalez A, Chase JH, et al.
PLoS One. 2013;8(1):e54703.

Characterization of the vaginal micro- and mycobiome in asymptomatic reproductive-age Estonian women.
Drell T, Lillsaar T, Tummeleht L, Simm J, et al.
PLoS One. 2013;8(1):e54379.

Whole-genome DNA methylation in skin lesions from patients with psoriasis vulgaris.
Zhang P, Zhao M, Liang G, Yin G, et al.
J Autoimmun. 2013 Jan 28. [Epub ahead of print]

Recessive MYL2 mutations cause infantile type I muscle fibre disease and cardiomyopathy.
Weterman MA, Barth PG, van Spaendonck-Zwarts KY, Aronica et al.
Brain. 2013 Jan;136(Pt 1):282-93.

Exome sequencing reveals SCO2 mutations in a family presented with fatal infantile hyperthermia.
Sambuughin N, Liu X, Bijarnia S, Wallace T, et al.
J Hum Genet. 2013 Jan 31. [Epub ahead of print]

Exome sequencing identifies novel rheumatoid arthritis-susceptible variants in the BTNL2.
Mitsunaga S, Hosomichi K, Okudaira Y, Nakaoka H, et al.
J Hum Genet. 2013 Jan 31. [Epub ahead of print]

Exome sequencing identifies SLC24A5 as a candidate gene for non-syndromic oculocutaneous albinism.
Wei AH, Zang DJ, Zhang Z, Liu XZ, et al.
J Invest Dermatol. 2013 Jan 30. [Epub ahead of print]

Feasibility study of semiconductor sequencing for noninvasive prenatal detection of fetal aneuploidy.
Yuan Y, Jiang F, Hua S, Du B, et al.
Clin Chem. 2013 Jan 30. [Epub ahead of print]

Direct sequencing and RipSeq interpretation as a tool for identification of polymicrobial infections.
Wolff TY, Eickhardt S, Björnsdottir MK, Moser C, et al.
J Clin Microbiol. 2013 Jan 30. [Epub ahead of print]

Sequencing-based genotyping of mixed human papillomavirus infections using RipSeq software.
Tardif KD, Simmon KE, Kommedal O, Pyne MT, Schlaberg R.
J Clin Microbiol. 2013 Jan 30. [Epub ahead of print]

Gut microbiomes of Malawian twin pairs discordant for Kwashiorkor.
Smith MI, Yatsunenko T, Manary MJ, Trehan I, et al.
Science. 2013 Jan 30. [Epub ahead of print]

Characterizing the emergence and persistence of drug resistant mutations in HIV-1 subtype C infections using 454 ultra deep pyrosequencing.
Bansode V, McCormack GP, Crampin AC, Ngwira B, et al.
BMC Infect Dis. 2013 Jan 30;13(1):52.

Comparison of targeted next-generation sequencing (NGS) and real-time PCR in the detection of EGFR, KRAS, and BRAF mutations on formalin-fixed, paraffin-embedded tumor material of non-small cell lung carcinoma-superiority of NGS.
Tuononen K, Mäki-Nevala S, Sarhadi VK, Wirtanen A, et al.
Genes Chromosomes Cancer. 2013 Jan 30. [Epub ahead of print]

Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma.
Zhao S, Choi M, Overton JD, Bellone S, et al.
Proc Natl Acad Sci U S A. 2013 Jan 28. [Epub ahead of print]

Recessive loss of function of the neuronal ubiquitin hydrolase UCHL1 leads to early-onset progressive neurodegeneration.
Bilguvar K, Tyagi NK, Ozkara C, Tuysuz B, et al.
Proc Natl Acad Sci U S A. 2013 Jan 28. [Epub ahead of print]

Rapid detection of aneuploidies on a benchtop sequencing platform.
Xie W, Tan Y, Li X, Lin G, et al.
Prenat Diagn. 2013 Jan 28:1-6.

The ADAMTS18 gene is responsible for autosomal recessive early onset severe retinal dystrophy.
Peluso I, Conte I, Testa F, Dharmalingam G, et al.
Orphanet J Rare Dis. 2013 Jan 28;8(1):16.

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.