Clinical Findings from Sequencing keep flowing…

Just a glance at GenomeWeb’s “In Print: Clinical Sequencing Papers of Note of the Last Two Weeks” is enough to show how hard it is to keep up with the sequencing revolution. Of the 37 publications mentioned here, 15 talk about whole-exome sequencing (WES) (and two amplicon sequencing and three whole-genome seq) identifying the causal variant(s).

Most of them use a slightly different way to align the reads, call variants and interpret the results. This reflects on the recent review paper in Bioinformatics journal (Tools for mapping high-throughput sequencing data) and the relevant blog post talking about the challenges of such a diverse tool-set (An embargo on short read alignment tools).

Amidst all this, the NGS Catalog is a wonderful tool to correlate technology with gene or disease or even specific mutations, along with author names and publications. So much data that can be mined for very useful snippets of information.

Thanks to the express permission of GenomeWeb editors, I am able to post below the list of papers highlighted in their section (which is behind a login access)

In Print: Clinical Sequencing Papers of Note of the Last Two Weeks

 ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia.
Jiang Q, Crews LA, Barrett CL, Chun HJ, et al.
Proc Natl Acad Sci U S A. 2012 Dec 28. [Epub ahead of print]

DGKE variants cause a glomerular microangiopathy that mimics membranoproliferative GN.
Ozaltin F, Li B, Rauhauser A, An SW, et al.
J Am Soc Nephrol. 2012 Dec 28. [Epub ahead of print]

Combining highly multiplexed PCR with semiconductor-based sequencing for rapid cancer genotyping.
Beadling C, Neff TL, Heinrich MC, Rhodes K, et al.
J Mol Diagn. 2012 Dec 27. [Epub ahead of print]

Next-generation sequencing reveals deep intronic cryptic ABCC8 and HADH splicing founder mutations causing hyperinsulinism by pseudoexon activation.
Flanagan SE, Xie W, Caswell R, Damhuis A, et al.
Am J Hum Genet. 2012 Dec 22. [Epub ahead of print]

Exome sequencing identifies INPPL1 mutations as a cause of opsismodysplasia.
Huber C, Faqeih EA, Bartholdi D, Bole-Feysot C, et al.
Am J Hum Genet. 2012 Dec 22. [Epub ahead of print]

Whole-genome analysis reveals that mutations in inositol polyphosphate phosphatase-like 1 cause opsismodysplasia.
Below JE, Earl DL, Shively KM, McMillin MJ, et al.
Am J Hum Genet. 2012 Dec 22. [Epub ahead of print]

Mitochondrial disease genetic diagnostics: optimized whole-exome analysis for all MitoCarta nuclear genes and the mitochondrial genome.
Falk MJ, Pierce EA, Consugar M, Xie MH, et al.
Discov Med. 2012 Dec;14(79):389-99.

Genetic diagnosis of autosomal dominant polycystic kidney disease by targeted capture and next-generation sequencing: Utility and limitations.
Qi XP, Du ZF, Ma JM, Chen XL, et al.
Gene. 2012 Dec 20. [Epub ahead of print]

RNA-seq reveals differentially expressed isoforms and novel splice variants in buccal mucosal cancer.
Jakhesara SJ, Koringa PG, Bhatt VD, Shah TM, et al.
Gene. 2012 Dec 20. [Epub ahead of print]

Next-generation sequencing identified new oncogenes and tumor suppressor genes in human hepatic tumors.
Amaddeo G, Guichard C, Imbeaud S, Zucman-Rossi J.
Oncoimmunology. 2012 Dec 1;1(9):1612-1613.

Exomic sequencing of medullary thyroid cancer reveals dominant and mutually exclusive oncogenic mutations in RET and RAS.
Agrawal N, Jiao Y, Sausen M, Leary R, et al.
J Clin Endocrinol Metab. 2012 Dec 21. [Epub ahead of print]

Newborn screening for SCID identifies patients with Ataxia telangiectasia.
Mallott J, Kwan A, Church J, Gonzalez-Espinosa D, et al.
J Clin Immunol. 2012 Dec 20. [Epub ahead of print]

Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia.
De Keersmaecker K, Atak ZK, Li N, Vicente C, et al.
Nat Genet. 2012 Dec 23. [Epub ahead of print]

Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas.
Palles C, Cazier JB, Howarth KM, Domingo E, et al.
Nat Genet. 2012 Dec 23. [Epub ahead of print]

Molecular diagnostics of a single multifocal non-small cell lung cancer case using targeted next generation sequencing.
Geurts-Giele WR, Dirkx-van der Velden AW, Bartalits NM, Verhoog LC, et al.
Virchows Arch. 2012 Dec 22. [Epub ahead of print]

Exome sequencing identifies mutations in CCDC114 as a cause of primary ciliary dyskinesia.
Knowles MR, Leigh MW, Ostrowski LE, Huang L, et al.
Am J Hum Genet. 2012 Dec 19. [Epub ahead of print]

Mutations in ECEL1 cause distal arthrogryposis type 5D.
McMillin MJ, Below JE, Shively KM, Beck AE, et al.
Am J Hum Genet. 2012 Dec 19. [Epub ahead of print]

Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis.
Diogo D, Kurreeman F, Stahl EA, Liao KP, et al.
Am J Hum Genet. 2012 Dec 19. [Epub ahead of print]

Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.
Michaelson JJ, Shi Y, Gujral M, Zheng H, et al.
Cell. 2012 Dec 21;151(7):1431-42.

RNA-seq analysis of synovial fibroblasts brings new insights into rheumatoid arthritis.
Heruth DP, Gibson M, Grigoryev DN, Zhang LQ, Ye SQ.
Cell Biosci. 2012 Dec 21;2(1):43.

Use of next generation sequencing technologies in research and beyond: are participants with mental health disorders fully protected?
Jaitovich Groisman I, Mathieu G, Godard B.
BMC Med Ethics. 2012 Dec 20;13(1):36.

Mutation of the PDGFRB gene as a cause of idiopathic basal ganglia calcification.
Nicolas G, Pottier C, Maltête D, Coutant S, et al.
Neurology. 2012 Dec 19. [Epub ahead of print]

Identification of TP53 as an acute lymphocytic leukemia susceptibility gene through exome sequencing.
Powell BC, Jiang L, Muzny DM, Treviño LR, et al.
Pediatr Blood Cancer. 2012 Dec 19. [Epub ahead of print]

Histamine-2 receptor blockers alter the fecal microbiota in premature infants.
Gupta RW, Tran L, Norori J, Ferris MJ, et al.
J Pediatr Gastroenterol Nutr. 2012 Dec 18. [Epub ahead of print]

Genome-wide sequencing for the identification of rearrangements associated with Tourette syndrome and obsessive-compulsive disorder.
Hooper SD, Johansson AC, Tellgren-Roth C, Stattin EL, et al.
BMC Med Genet. 2012 Dec 19;13(1):123.

Detection of BCR-ABL1 mutations in chronic myeloid leukaemia by massive parallel sequencing.
Eyal E, Amir A, Cesarkas K, Jacob-Hirsch J, et al.
Br J Haematol. 2012 Dec 17. [Epub ahead of print]

West syndrome caused by ST3Gal-III deficiency.
Edvardson S, Baumann AM, Mühlenhoff M, Stephan O, et al.
Epilepsia. 2012 Dec 17. [Epub ahead of print]

Exome sequencing identifies a founder frameshift mutation in an alternative exon of USH1C as the cause of autosomal recessive retinitis pigmentosa with late-onset hearing loss.
Khateb S, Zelinger L, Ben-Yosef T, Merin S, et al.
PLoS One. 2012;7(12):e51566.

The ChIP-seq-defined networks of Bcl-3 gene binding support its required role in skeletal muscle atrophy.
Jackman RW, Wu CL, Kandarian SC.
PLoS One. 2012;7(12):e51478.

Characterization and validation of insertions and deletions in 173 patient exomes.
Lescai F, Bonfiglio S, Bacchelli C, Chanudet E, et al.
PLoS One. 2012;7(12):e51292.

Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes.
Feliubadaló L, Lopez-Doriga A, Castellsagué E, Del Valle J, et al.
Eur J Hum Genet. 2012 Dec 19. [Epub ahead of print]

A compound heterozygous mutation in DPAGT1 results in a congenital disorder of glycosylation with a relatively mild phenotype.
Iqbal Z, Shahzad M, Vissers LE, van Scherpenzeel M, et al.
Eur J Hum Genet. 2012 Dec 19. [Epub ahead of print]

Analysis of a Chinese pedigree with Zellweger syndrome reveals a novel PEX1 mutation by next-generation sequencing.
Sun Y, Wang L, Wei X, Zhu Q, et al.
Clin Chim Acta. 2012 Dec 13. [Epub ahead of print]

Filling the gaps — the generation of full genomic sequences for 15 common and well-documented HLA class I alleles using next-generation sequencing technology.
Lind C, Ferriola D, Mackiewicz K, Sasson A, Monos D.
Hum Immunol. 2012 Dec 12. [Epub ahead of print]

Integrating GWAS and expression data for functional characterization of disease-associated SNPs: an application to follicular lymphoma.
Conde L, Bracci PM, Richardson R, Montgomery SB, Skibola CF.
Am J Hum Genet. 2012 Dec 11. [Epub ahead of print]

Whole-exome sequencing identifies LRIT3 mutations as a cause of autosomal-recessive complete congenital stationary night blindness.
Zeitz C, Jacobson SG, Hamel CP, Bujakowska K, et al.
Am J Hum Genet. 2012 Dec 11. [Epub ahead of print]

Exome sequencing reveals a signal transducer and activator of transcription 1 (STAT1) mutation in a child with recalcitrant cutaneous fusariosis.
Wang X, Lin Z, Gao L, Wang A, et al.
J Allergy Clin Immunol. 2012 Dec 13. [Epub ahead of print]
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