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In Print: Last Week's Clinical Sequencing Papers of Note: Jan 30, 2013


Novel KLK4 and MMP20 mutations discovered by whole-exome sequencing.
Wang SK, Hu Y, Simmer JP, Seymen F, et al.
Dent Res. 2013 Jan 25. [Epub ahead of print]

Haploinsufficiency of KDM6A is associated with severe psychomotor retardation, global growth restriction, seizures and cleft palate.
Lindgren AM, Hoyos T, Talkowski ME, Hanscom C, et al.
Hum Genet. 2013 Jan 25. [Epub ahead of print]

Characterization of placenta-specific microRNAs in fetal growth restriction pregnancy.
Higashijima A, Miura K, Mishima H, Kinoshita A, et al.
Prenat Diagn. 2013 Jan 27:1-9.

Reduced dosage of ERF causes complex craniosynostosis in humans and mice and links ERK1/2 signaling to regulation of osteogenesis.
Twigg SR, Vorgia E, McGowan SJ, Peraki I, et al.
Nat Genet. 2013 Jan 27. [Epub ahead of print]

Mutations in TCF12, encoding a basic helix-loop-helix partner of TWIST1, are a frequent cause of coronal craniosynostosis.
Sharma VP, Fenwick AL, Brockop MS, McGowan SJ, et al.
Nat Genet. 2013 Jan 27. [Epub ahead of print]

Mutations in DNA2 link progressive myopathy to mitochondrial DNA instability.
Ronchi D, Di Fonzo A, Lin W, Bordoni A, et al.
Am J Hum Genet. 2013 Jan 22. [Epub ahead of print]

Using whole-exome sequencing to identify inherited causes of autism.
Yu TW, Chahrour MH, Coulter ME, Jiralerspong S, et al.
Neuron. 2013 Jan 23;77(2):259-273.
(See our coverage of this paper in last week's issue here.)

Rare complete knockouts in humans: population distribution and significant role in autism spectrum disorders.
Lim ET, Raychaudhuri S, Sanders SJ, Stevens C, et al.
Neuron. 2013 Jan 23;77(2):235-42.
(See our coverage of this paper in last week's issue here.)

Comparison of population and 454 "deep" sequence analysis for HIV-1 tropism versus the original trofile assay in non-B subtypes.
Lee GQ, Harrigan PR, Dong W, Poon A, et al.
AIDS Res Hum Retroviruses. 2013 Jan 25. [Epub ahead of print]

RNA-seq for enrichment and analysis of IRF5 transcript expression in SLE.
Stone RC, Du P, Feng D, Dhawan K, et al.
PLoS One. 2013;8(1):e54487.

Simultaneous sequencing of 24 genes associated with steroid-resistant nephrotic syndrome.
McCarthy HJ, Bierzynska A, Wherlock M, Ognjanovic M, et al.
Clin J Am Soc Nephrol. 2013 Jan 24. [Epub ahead of print]

Massively parallel sequencing for chromosomal abnormality testing in trophectoderm cells of human blastocysts.
Yin X, Tan K, Vajta G, Jiang H, et al.
Biol Reprod. 2013 Jan 24. [Epub ahead of print]

Whole exome sequencing identifies a mutation for a novel form of corneal intraepithelial dyskeratosis.
Soler VJ, Tran-Viet KN, Galiacy SD, Limviphuvadh V, et al.
J Med Genet. 2013 Jan 24. [Epub ahead of print]

Mutations in TMEM231 cause Meckel-Gruber syndrome.
Shaheen R, Ansari S, Al Mardawi E, Alshammari MJ, Alkuraya FS.
J Med Genet. 2013 Jan 24. [Epub ahead of print]

Two-phase designs to follow-up genome-wide association signals with DNA resequencing studies.
Schaid DJ, Jenkins GD, Ingle JN, Weinshilboum RM.
Genet Epidemiol. 2013 Jan 24. [Epub ahead of print]

TERT promoter mutations in familial and sporadic melanoma.
Horn S, Figl A, Rachakonda PS, Fischer C, et al.
Science. 2013 Jan 24. [Epub ahead of print]

Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-seq data.
Ding M, Wang H, Chen J, Shen B, Xu Z.
Comput Math Methods Med. 2012;2012:568950.

NGS identifies TAZ mutation in a family with X-linked dilated cardiomyopathy.
Man E, Lafferty KA, Funke BH, Lun KS, et al.
BMJ Case Rep. 2013 Jan 22;2013. pii: bcr2012007529.

Deep sequencing reveals abundant noncanonical retroviral microRNAs in B-cell leukemia/lymphoma.
Rosewick N, Momont M, Durkin K, Takeda H, et al.
Proc Natl Acad Sci U S A. 2013 Jan 23. [Epub ahead of print]

Half or more of the somatic mutations in cancers of self-renewing tissues originate prior to tumor initiation.
Tomasetti C, Vogelstein B, Parmigiani G.
Proc Natl Acad Sci U S A. 2013 Jan 23. [Epub ahead of print]

DNA-mutation Inventory to Refine and Enhance Cancer Treatment (DIRECT): A catalogue of clinically relevant cancer mutations to enable genome-directed cancer therapy.
Yeh P, Chen H, Andrews J, Naser R, et al.
Clin Cancer Res. 2013 Jan 23. [Epub ahead of print]

TBC1D24 truncating mutation resulting in severe neurodegeneration.
Guven A, Tolun A.
J Med Genet. 2013 Jan 23. [Epub ahead of print]

Tracking the evolution of dengue virus strains D2S10 and D2S20 by 454 pyrosequencing.
Makhluf H, Buck MD, King K, Perry ST, et al.
PLoS One. 2013;8(1):e54220.

Metagenomic analysis of subgingival microbiota following non-surgical periodontal therapy: a pilot study.
Laksmana T, Kittichotirat W, Huang Y, Chen W, et al.
Open Dent J. 2012;6:255-61.

Predicting Mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies.
Li MX, Kwan JS, Bao SY, Yang W, et al.
PLoS Genet. 2013 Jan;9(1):e1003143.

Extensive changes in DNA methylation are associated with expression of mutant huntingtin.
Ng CW, Yildirim F, Yap YS, Dalin S, et al.
Proc Natl Acad Sci U S A. 2013 Jan 22. [Epub ahead of print]

The molecular profile of adult T-cell acute lymphoblastic leukemia: Mutations in RUNX1 and DNMT3A are associated with poor prognosis in T-ALL.
Grossmann V, Haferlach C, Weissmann S, Roller A, et al.
Genes Chromosomes Cancer. 2013 Jan 23. [Epub ahead of print]

Hereditary uveal melanoma: A report of a germline mutation in BAP1.
Höiom V, Edsgärd D, Helgadottir H, Eriksson H, et al.
Genes Chromosomes Cancer. 2013 Jan 23. [Epub ahead of print]

Frontotemporal dementia-amyotrophic lateral sclerosis syndrome locus on chromosome 16p12.1-q12.2: genetic, clinical and neuropathological analysis.
Dobson-Stone C, Luty AA, Thompson EM, Blumbergs P, et al.
Acta Neuropathol. 2013 Jan 22. [Epub ahead of print]

The Scan

CDC Calls Delta "Variant of Concern"

CNN reports the US Centers for Disease Control and Prevention now considers the Delta variant of SARS-CoV-2 to be a "variant of concern."

From FDA to Venture Capital

Former FDA Commissioner Stephen Hahn is taking a position at a venture capital firm, leading some ethicists to raise eyebrows, according to the Washington Post.

Consent Questions

Nature News writes that there are questions whether informed consent was obtained for some submissions to a database of Y-chromosome profiles.

Cell Studies on Multimodal Single-Cell Analysis, Coronaviruses in Bats, Urban Microbiomes

In Cell this week: approach to analyze multimodal single-cell genomic data, analysis of bat coronaviruses, and more.