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In Print: Last Week's Clinical Sequencing Papers of Note: Jan 25, 2012


The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients.
Jiang Z, Jhunjhunwala S, Liu J, Haverty PM, et al.
Genome Res. 2012 Jan 20. [Epub ahead of print]

Mutations in kelch-like 3 and cullin 3 cause hypertension and electrolyte abnormalities.
Boyden LM, Choi M, Choate KA, Nelson-Williams CJ, et al.
Nature. 2012 Jan 22. [Epub ahead of print]

Next-generation sequencing identifies TGF-β1-associated gene expression profiles in renal epithelial cells reiterated in human diabetic nephropathy.
Brennan EP, Morine MJ, Walsh DW, Roxburgh SA, et al.
Biochim Biophys Acta. 2012 Jan 14. [Epub ahead of print]

Evaluating the genomic and sequence integrity of human ES cell lines; comparison to normal genomes.
Funk WD, Labat I, Sampathkumar J, Gourraud PA, et al.
Stem Cell Res. 2012 Mar;8(2):154-64.

Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations.
Rausch T, Jones DT, Zapatka M, Stütz AM, et al.
Cell. 2012 Jan 20;148(1-2):59-71.

De novo mutations of the gene encoding the histone acetyltransferase KAT6B cause genitopatellar syndrome.
Simpson MA, Deshpande C, Dafou D, Vissers LE, et al.
Am J Hum Genet. 2012 Jan 18. [Epub ahead of print]

RHBDF2 mutations are associated with tylosis, a familial esophageal cancer syndrome.
Blaydon DC, Etheridge SL, Risk JM, Hennies HC, et al.
Am J Hum Genet. 2012 Jan 18. [Epub ahead of print]

Mutations in SRCAP, encoding SNF2-related CREBBP activator protein, cause floating-harbor syndrome.
Hood RL, Lines MA, Nikkel SM, Schwartzentruber J, et al.
Am J Hum Genet. 2012 Jan 18. [Epub ahead of print]

Mutations in KAT6B, encoding a histone acetyltransferase, cause genitopatellar syndrome.
Campeau PM, Kim JC, Lu JT, Schwartzentruber JA, et al.
Am J Hum Genet. 2012 Jan 18. [Epub ahead of print]

Exome sequencing identifies KIAA1377 and C5orf42 as susceptibility genes for monomelic amyotrophy.
Lim YM, Koh I, Park YM, Kim JJ, et al.
Neuromuscul Disord. 2012 Jan 18. [Epub ahead of print]

IGFBP-4 tumor and serum levels are increased across all stages of epithelial ovarian cancer.
Mosig RA, Lobl M, Senturk E, Shah H, et al.
J Ovarian Res. 2012 Jan 20;5(1):3. [Epub ahead of print]

Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis.
Coppieters F, Wilde BD, Lefever S, Meester ED, et al.
Genet Med. 2012 Jan 19. [Epub ahead of print]

High resolution clustering of Salmonella enterica serovar Montevideo strains using a next-generation sequencing approach.
Allard MW, Luo Y, Strain E, Li C, et al.
BMC Genomics. 2012 Jan 19;13(1):32. [Epub ahead of print]

Genomic analysis uncovers a phenotypically diverse but genetically homogeneous Escherichia coli ST131 clone circulating in unrelated urinary tract infections.
Clark G, Paszkiewicz K, Hale J, Weston V, et al.
J Antimicrob Chemother. 2012 Jan 18. [Epub ahead of print]

KIF1A missense mutations in SPG30, an autosomal recessive spastic paraplegia: distinct phenotypes according to the nature of the mutations.
Klebe S, Lossos A, Azzedine H, Mundwiller E, et al.
Eur J Hum Genet. 2012 Jan 18. [Epub ahead of print]

Discovery of variants unmasked by hemizygous deletions.
Hochstenbach R, Poot M, Nijman IJ, Renkens I, et al.
Eur J Hum Genet. 2012 Jan 18. [Epub ahead of print]

Characterization of mtDNA variation in a cohort of South African paediatric patients with mitochondrial disease.
van der Walt EM, Smuts I, Taylor RW, Elson JL, et al.
Eur J Hum Genet. 2012 Jan 18. [Epub ahead of print]

Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA.
Mastrokolias A, den Dunnen JT, van Ommen GB, 't Hoen PA, van Roon-Mom WM.
BMC Genomics. 2012 Jan 18;13(1):28. [Epub ahead of print]

Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenine phosphorylase (MTAP), an exploitable tumor target.
Collins CC, Volik SV, Lapuk A, Wang Y, et al.
Mol Cancer Ther. 2012 Jan 17. [Epub ahead of print]

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.