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Last Week's Clinical Sequencing Papers of Note: Apr 1, 2014

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Differences in the composition of the human antibody repertoire by B cell subsets in the blood.
Mroczek ES, Ippolito GC, Rogosch T, Hoi KH, et al.
Front Immunol. 2014 Mar 19;5:96.


A176: deep sequencing reveals differential small RNA expression in serum exosomes of children with juvenile idiopathic arthritis.
Jiang K, Hu Z, Chen Y, Jarvis JN.
Arthritis Rheumatol. 2014 Mar;66 Suppl 11:S230.


A157: Macrophage Activation Syndrome-like Illness Due to an Activating Mutation in NLRC4.
Canna S, de Jesus AA, Deng Z, Gouni S, et al.
Arthritis Rheumatol. 2014 Mar;66 Suppl 11:S203.


A121: in search of infectious triggers of periodic Fever, aphthous stomatitis, pharyngitis and adenitis syndrome.
Freeman S, Bhatt A, Pedamallu C, King S, et al.
Arthritis Rheumatol. 2014 Mar;66 Suppl 11:S158.


A119: deep sequencing analysis of the T regulatory and T effector repertoire in juvenile idiopathic arthritis.
Henderson LA, Volpi S, Frugoni F, Kim S, et al.
Arthritis Rheumatol. 2014 Mar;66 Suppl 11:S156.


Jannovar: A Java Library for Exome Annotation.
Jäger M, Wang K, Bauer S, Smedley D, et al.
Hum Mutat. 2014 Feb 17. [Epub ahead of print]


Early presentation of cystic kidneys in a family with a homozygous INVS mutation.
Oud MM, van Bon BW, Bongers EM, Hoischen A, et al.
Am J Med Genet A. 2014 Mar 26. [Epub ahead of print]


Identification of Novel Transcription Factors in Osteoclast Differentiation using Genome-wide Analysis of Open Chromatin Determined by DNase-seq.
Inoue K, Imai Y.
J Bone Miner Res. 2014 Mar 28. [Epub ahead of print]


Fast and Robust Next-Generation Sequencing Technique Using Ion Torrent Personal Genome Machine for the Screening of Neurofibromatosis Type 1 (NF1) Gene.
Balla B, Arvai K, Horváth P, Tobiás B, et al.
J Mol Neurosci. 2014 Mar 28. [Epub ahead of print]


Theoretical performance of non-invasive prenatal testing for chromosome imbalances using counting of cell-free DNA fragments in maternal plasma.
Benn P, Cuckle H.
Prenat Diagn. 2014 Mar 27. [Epub ahead of print]


Opportunities and challenges of next-generation DNA sequencing for breast units.
Pilgrim SM, Pain SJ, Tischkowitz MD.
Br J Surg. 2014 Mar 27. [Epub ahead of print]


Mutations in the Gene That Encodes the F-Actin Binding Protein Anillin Cause FSGS.
Gbadegesin RA, Hall G, Adeyemo A, Hanke N, et al.
J Am Soc Nephrol. 2014 Mar 27. [Epub ahead of print]


Mutations in PAX2 Associate with Adult-Onset FSGS.
Barua M, Stellacci E, Stella L, Weins A, et al.
J Am Soc Nephrol. 2014 Mar 27. [Epub ahead of print]


Neurofibromatosis Type 1 Gene Mutation Analysis Using Sequence Capture and High-throughput Sequencing.
Uusitalo E, Hammais A, Palonen E, Brandt A, et al.
Acta Derm Venereol. 2014 Mar 25. [Epub ahead of print]


Expanding the phenotype of mutations in DICER1: mosiac missense mutations in the RNase IIIb domain of DICER1 cause GLOW syndrome.
Klein S, Lee H, Ghahremani S, Kempert P, et al.
J Med Genet. 2014 Mar 27. [Epub ahead of print]


Changes in Colorectal Carcinoma Genomes under Anti-EGFR Therapy Identified by Whole-Genome Plasma DNA Sequencing.
Mohan S, Heitzer E, Ulz P, Lafer I, et al.
PLOS Genet. 2014 Mar 27;10(3):e1004271.


Heterozygous De Novo and Inherited Mutations in the Smooth Muscle Actin (ACTG2) Gene Underlie Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome.
Wangler MF, Gonzaga-Jauregui C, Gambin T, Penney S, et al.
PLOS Genet. 2014 Mar 27;10(3):e1004258.


Bacterial Profile of Dentine Caries and the Impact of pH on Bacterial Population Diversity.
Kianoush N, Adler CJ, Nguyen KA, Browne GV, et al.
PLOS One. 2014 Mar 27;9(3):e92940.


CDKN2D-WDFY2 Is a Cancer-Specific Fusion Gene Recurrent in High-Grade Serous Ovarian Carcinoma.
Kannan K, Coarfa C, Rajapakshe K, Hawkins SM, et al.
PLOS Genet. 2014 Mar 27;10(3):e1004216.


A single center's experience with noninvasive prenatal testing.
Beamon CJ, Hardisty EE, Harris SC, Vora NL.
Genet Med. 2014 Mar 27. [Epub ahead of print]


Deep sequencing with intronic capture enables identification of an APC exon 10 inversion in a patient with polyposis.
Shirts BH, Salipante SJ, Casadei S, Ryan S, et al.
Genet Med. 2014 Mar 27. [Epub ahead of print]


Biallelic DICER1 mutations in sporadic pleuropulmonary blastoma.
Seki M, Yoshida K, Shiraishi Y, Shimamura T, et al.
Cancer Res. 2014 Mar 27. [Epub ahead of print]


Detection of an activated JAK3 variant and a Xq26.3 microdeletion causing loss of PHF6 and miR-424 expression in myelodysplastic syndromes by combined targeted next generation sequencing and SNP array analysis.
Kunze K, Gamerdinger U, Leßig-Owlanj J, Sorokina M, et al.
Pathol Res Pract. 2014 Feb 23. [Epub ahead of print]


Sensitive and specific detection of EML4-ALK rearrangements in non-small cell lung cancer (NSCLC) specimens by multiplex amplicon RNA massive parallel sequencing.
Moskalev EA, Frohnauer J, Merkelbach-Bruse S, Schildhaus HU, et al.
Lung Cancer. 2014 Mar 13. [Epub ahead of print]


Whole transcriptome sequencing of a paediatric case of de novo acute myeloid leukaemia with del(5q) reveals RUNX1-USP42 and PRDM16-SKI fusion transcripts.
Masetti R, Togni M, Astolfi A, Pigazzi M, et al.
Br J Haematol. 2014 Mar 27. [Epub ahead of print]


Views of Primary Care Providers Regarding the Return of Genome Sequencing Incidental Findings.
Strong KA, Zusevics KL, Bick D, Veith R.
Clin Genet. 2014 Mar 27. [Epub ahead of print]


Mining genome sequencing data to identify the genomic features linked to breast cancer histopathology.
Ping Z, Siegal GP, Almeida JS, Schnitt SJ, Shen D.
J Pathol Inform. 2014 Jan 31;5:3.


Massive parallel sequencing provides new perspectives on bacterial brain abscesses.
Kommedal O, Wilhelmsen MT, Skrede S, Meisal R, et al.
J Clin Microbiol. 2014 Mar 26. [Epub ahead of print]


Genetic Counselors' Views and Experiences with the Clinical Integration of Genome Sequencing.
Machini K, Douglas J, Braxton A, Tsipis J, Kramer K.
J Genet Couns. 2014 Mar 28. [Epub ahead of print]


Mutation in KANK2, encoding a sequestering protein for steroid receptor coactivators, causes keratoderma and woolly hair.
Ramot Y, Molho-Pessach V, Meir T, Alper-Pinus R, et al.
J Med Genet. 2014 Mar 26. [Epub ahead of print]


Frequent mutations in chromatin-remodelling genes in pulmonary carcinoids.
Fernandez-Cuesta L, Peifer M, Lu X, Sun R, et al.
Nat Commun. 2014 Mar 27;5:3518.


SLC7A14 linked to autosomal recessive retinitis pigmentosa.
Jin ZB, Huang XF, Lv JN, Xiang L, et al.
Nat Commun. 2014 Mar 27;5:3517.


REST and stress resistance in ageing and Alzheimer's disease.
Lu T, Aron L, Zullo J, Pan Y, et al.
Nature. 2014 Mar 27;507(7493):448-54.


Whole-genome sequencing in newborn screening programs.
Knoppers BM, Sénécal K, Borry P, Avard D.
Sci Transl Med. 2014 Mar 26;6(229):229cm2.


Identification of genomic alterations in oesophageal squamous cell cancer.
Song Y, Li L, Ou Y, Gao Z, et al.
Nature. 2014 Mar 16. [Epub ahead of print]


Whole exome sequencing implicates PTCH1 and COL17A1 genes in ossification of the posterior longitudinal ligament of the cervical spine in Chinese patients.
Wei W, He HL, Chen CY, Zhao Y, et al.
Genet Mol Res. 2014 Mar 17;13(1):1794-804.


Whole genome sequencing identifies a novel occludin mutation in microcephaly with band-like calcification and polymicrogyria that extends the phenotypic spectrum.
Elsaid MF, Kamel H, Chalhoub N, Aziz NA, et al.
Am J Med Genet A. 2014 Mar 25. [Epub ahead of print]


Novel homozygous DEAF1 variant suspected in causing white matter disease, intellectual disability, and microcephaly.
Faqeih EA, Al-Owain M, Colak D, Kenana R, et al.
Am J Med Genet A. 2014 Mar 25. [Epub ahead of print]


Novel insight into mutational landscape of head and neck squamous cell carcinoma.
Gaykalova DA, Mambo E, Choudhary A, Houghton J, et al.
PLOS One. 2014 Mar 25;9(3):e93102.


Analysis of the whole mitochondrial genome: translation of the Ion Torrent Personal Genome Machine system to the diagnostic bench?
Seneca S, Vancampenhout K, Van Coster R, Smet J, et al.
Eur J Hum Genet. 2014 Mar 26. [Epub ahead of print]


Confined placental origin of the circulating cell free fetal DNA revealed by a discordant non-invasive prenatal test result in a trisomy 18 pregnancy.
Mao J, Wang T, Wang BJ, Liu YH, et al.
Clin Chim Acta. 2014 Mar 22. [Epub ahead of print]


An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.
Brownstein CA, Beggs AH, Homer N, Merriman B, et al.
Genome Biol. 2014 Mar 25;15(3):R53.


Segmental overgrowth syndrome due to an activating PIK3CA mutation identified in affected muscle tissue by exome sequencing.
Rasmussen M, Sunde L, Weigert KP, Bogaard PW, Lildballe DL.
Am J Med Genet A. 2014 Mar 24. [Epub ahead of print]


Diagnostic Exome Sequencing and Tailored Bioinformatics of the Parents of a Deceased Child with Cobalamin Deficiency Suggests Digenic Inheritance of the MTR and LMBRD1 Genes.
Gonzalez KD, Li X, Lu HM, Lu H, et al.
JIMD Rep. 2014 Mar 25. [Epub ahead of print]


Genetic Counseling Practice in Next Generation Sequencing Research: Implications for the Ethical Oversight of the Informed Consent Process.
Egalite N, Groisman IJ, Godard B.
J Genet Couns. 2014 Mar 25. [Epub ahead of print]


IROme, a New High-Throughput Molecular Tool for the Diagnosis of Inherited Retinal Dystrophies-A Price Comparison with Sanger Sequencing.
Schorderet DF, Bernasconi M, Tiab L, Favez T, Escher P.
Adv Exp Med Biol. 2014;801:171-6.


Mutation K42E in Dehydrodolichol Diphosphate Synthase (DHDDS) Causes Recessive Retinitis Pigmentosa.
Lam BL, Züchner SL, Dallman J, Wen R, et al.
Adv Exp Med Biol. 2014;801:165-70.


Application of Next-Generation Sequencing to Identify Genes and Mutations Causing Autosomal Dominant Retinitis Pigmentosa (adRP).
Daiger SP, Bowne SJ, Sullivan LS, Blanton SH, et al.
Adv Exp Med Biol. 2014;801:123-9.


Copy number alterations and neoplasia-specific mutations in MELK, PDCD1LG2, TLN1, and PAX5 at 9p in different neoplasias.
Sarhadi VK, Lahti L, Scheinin I, Ellonen P, et al.
Genes Chromosomes Cancer. 2014 Mar 24. [Epub ahead of print]


Identification of a novel missense mutation of MAF in a Japanese family with congenital cataract by whole exome sequencing: A clinical report and review of literature.
Narumi Y, Nishina S, Tokimitsu M, Aoki Y, et al.
Am J Med Genet A. 2014 Mar 24. [Epub ahead of print]


Profiling Cancer Gene Mutations in Clinical Formalin-Fixed, Paraffin-Embedded Colorectal Tumor Specimens Using Targeted Next-Generation Sequencing.
Zhang L, Chen L, Sah S, Latham GJ, et al.
Oncologist. 2014 Mar 24. [Epub ahead of print]


NOTCH1 Mutations Occur Early During Cutaneous Squamous Cell Carcinogenesis.
South AP, Purdie KJ, Watt SA, Haldenby S, et al.
J Invest Dermatol. 2014 Mar 24. [Epub ahead of print]


Effective Variant Detection by Targeted Deep Sequencing of DNA Pools: An Example from Parkinson's Disease.
Pihlstrøm L, Rengmark A, Bjørnarå KA, Toft M.
Ann Hum Genet. 2014 Mar 24. [Epub ahead of print]

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.