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In Print: Last Week's Clinical Sequencing Papers of Note: Jun 6, 2012


Exome sequencing and genetic testing for MODY.
Johansson S, Irgens H, Chudasama KK, Molnes J, et al.
PLoS One. 2012;7(5):e38050.

ColoSeq provides comprehensive Lynch and polyposis syndrome mutational analysis using massively parallel sequencing.
Pritchard CC, Smith C, Salipante SJ, Lee MK, et al.
J Mol Diagn. 2012 May 29. [Epub ahead of print]

Somatic mosaic activating mutations in PIK3CA cause CLOVES syndrome.
Kurek KC, Luks VL, Ayturk UM, Alomari AI, et al.
Am J Hum Genet. 2012 May 30. [Epub ahead of print]

Deep sequence analysis of non-small cell lung cancer: integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations.
Kalari KR, Rossell D, Necela BM, Asmann YW, et al.
Front Oncol. 2012;2:12.

Full-exon pyrosequencing screening of BRCA germline mutations in Mexican women with inherited breast and ovarian cancer.
Vaca-Paniagua F, Alvarez-Gomez RM, Fragoso-Ontiveros V, Vidal-Millan S, et al.
PLoS One. 2012;7(5):e37432.

Whole-exome sequencing and an iPSC-derived cardiomyocyte model provides a powerful platform for gene discovery in left ventricular hypertrophy.
Zhi D, Irvin MR, Gu CC, Stoddard AJ, et al.
Front Genet. 2012;3:92.

Use of mutation profiles to refine the classification of endometrial carcinomas.
McConechy MK, Ding J, Cheang MC, Wiegand K, et al.
J Pathol. 2012 May 31. [Epub ahead of print]

Mutation in RAB33B, which encodes a regulator of retrograde Golgi transport, defines a second Dyggve-Melchior-Clausen locus.
Alshammari MJ, Al-Otaibi L, Alkuraya FS.
J Med Genet. 2012 May 31. [Epub ahead of print]

IMGT/HighV-QUEST: the IMGT web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.
Alamyar E, Giudicelli V, Li S, Duroux P, Lefranc MP.
Immunome Res. 2012 Apr 20;8(1):26.

Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma.
Weiss GJ, Liang WS, Izatt T, Arora S, et al.
PLoS One. 2012;7(5):e37029.

GATA2 zinc finger 1 mutations associated with biallelic CEBPA mutations define a unique genetic entity of acute myeloid leukemia.
Greif PA, Dufour A, Konstandin NP, Ksienzyk B, et al.
Blood. 2012 May 30. [Epub ahead of print]

Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA.
Forshew T, Murtaza M, Parkinson C, Gale D, et al.
Sci Transl Med. 2012 May 30;4(136):136ra68.

Dramatic reduction of sequence artefacts from DNA isolated from formalin-fixed cancer biopsies by treatment with uracil-DNA glycosylase.
Do H, Dobrovic A.
Oncotarget. 2012 May 24. [Epub ahead of print]

Quantifying selection in high-throughput immunoglobulin sequencing data sets.
Yaari G, Uduman M, Kleinstein SH.
Nucleic Acids Res. 2012 May 27. [Epub ahead of print]

The Scan

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.