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Clinical Sequencing Papers of Note: Jul 12, 2011


Increased exonic de novo mutation rate in individuals with schizophrenia.
Girard SL, Gauthier J, Noreau A, et al.
Nat Genet. 2011 Jul 10. [Epub ahead of print]

Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.
Saulnier DM, Riehle K, Mistretta TA, et al.
Gastroenterology. 2011 Jul 7. [Epub ahead of print]

Uncovering the profile of somatic mtDNA mutations in Chinese colorectal cancer patients.
Wang CY, Li H, Hao XD, Liu J, et al.
PLoS One. 2011;6(6):e21613. Epub 2011 Jun 28.

Comparative cenomics and transcriptomics of Propionibacterium acnes.
Brzuszkiewicz E, Weiner J, Wollherr A, et al.
PLoS One. 2011;6(6):e21581. Epub 2011 Jun 27.

Exome sequencing identifies CCDC8 mutations in 3-M syndrome, suggesting that CCDC8 contributes in a pathway with CUL7 and OBSL1 to control human growth.
Hanson D, Murray PG, O'Sullivan J, et al.
Am J Hum Genet. 2011 Jul 5. [Epub ahead of print]

Two-stage design of sequencing studies for testing association with rare variants.
Yang F, Thomas DC.
Hum Hered. 2011 Jul 2;71(4):209-220. [Epub ahead of print]

A new expectation-maximization statistical test for case-control association studies considering rare variants obtained by high-throughput sequencing.
Gordon D, Finch SJ, De La Vega F.
Hum Hered. 2011;71(2):113-25. Epub 2011 Jul 6.

Deep sequencing of the human TCR{gamma} and TCR{beta} repertoires suggests that TCR{beta} rearranges after {alpha}{beta} and {gamma}{delta} T cell commitment.
Sherwood AM, Desmarais C, Livingston RJ, et al.
Sci Transl Med. 2011 Jul 6;3(90):90ra61.

Genome-wide profiling of chromatin signatures reveals epigenetic regulation of microRNA genes in colorectal cancer.
Suzuki H, Takatsuka S, Akashi H, et al.
Cancer Res. 2011 Jul 6. [Epub ahead of print]

Gain-of-function human STAT1 mutations impair IL-17 immunity and underlie chronic mucocutaneous candidiasis.
Liu L, Okada S, Kong XF, et al.
J Exp Med. 2011 Jul 4. [Epub ahead of print]

Genome sequencing reveals unique mutations in characteristic metabolic pathways and the transfer of virulence genes between V. mimicus and V. cholerae.
Wang D, Wang H, Zhou Y, et al.
PLoS One. 2011;6(6):e21299. Epub 2011 Jun 22.

A comprehensive survey of miRNA repertoire and 3' addition events in the placentas of patients with pre-eclampsia from high-throughput sequencing.
Guo L, Yang Q, Lu J, Li H, Ge Q, Gu W, Bai Y, Lu Z.
PLoS One. 2011;6(6):e21072. Epub 2011 Jun 22.

Poly (A) transcriptome assessment of ERBB2-induced alterations in breast cell lines.
Carraro DM, Ferreira EN, de Campos Molina G, et al.
PLoS One. 2011;6(6):e21022. Epub 2011 Jun 22.

Detection of inferred CCR5- and CXCR4-using HIV-1 variants and evolutionary intermediates using ultra-deep pyrosequencing.
Bunnik EM, Swenson LC, Edo-Matas D, et al.
PLoS Pathog. 2011 Jun;7(6):e1002106. Epub 2011 Jun 23.

Motivators for participation in a whole-genome sequencing study: implications for translational genomics research.
Facio FM, Brooks S, Loewenstein J, et al.
Eur J Hum Genet. 2011 Jul 6. [Epub ahead of print]

Advancing a clinically relevant perspective of the clonal nature of cancer.
Ruiz C, Lenkiewicz E, Evers L, et al.
Proc Natl Acad Sci U S A. 2011 Jul 5. [Epub ahead of print]

Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data.
Tao Y, Ruan J, Yeh SH, et al.
Proc Natl Acad Sci U S A. 2011 Jul 5. [Epub ahead of print]

Diverse mutational mechanisms cause pathogenic subtelomeric rearrangements.
Luo Y, Hermetz KE, Jackson JM, et al.
Hum Mol Genet. 2011 Jul 4. [Epub ahead of print]

The Scan

Long COVID-19 Susceptibility Clues Contained in Blood Plasma Proteome

A longitudinal study in eBioMedicine found weeks-long blood plasma proteome shifts after SARS-CoV-2 infection, along with proteomic signatures that appeared to coincide with long Covid risk.

Tibetan Study Finds Adaptive Variant Influencing Skin Pigmentation

With a combination of phenotyping and genetic data, researchers document at PNAS a Tibetan-enriched enhancer variant influencing melanin synthesis and ultraviolet light response.

Domestication Linked to Nervous System Genes in Inbred Mouse Strains

Researchers highlighted more than 300 positively selected genes in domesticated mice, including genes linked to nervous system function or behavior in Genome Biology.

ALS Genetic Testing May Be Informative Across Age Ranges, Study Finds

Researchers in the journal Brain identified clinically actionable variants in a significant subset of older ALS patients, prompting them to point to the potential benefits of broader test use.