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Recent Clinical Sequencing Papers of Note: Oct 1, 2014

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Challenges in evaluating next-generation sequence data for clinical decisions.
Williams JK, Cashion AK, Veenstra DL.
Nurs Outlook. 2014 Aug 23. [Epub ahead of print]


Gatekeepers or intermediaries? The role of clinicians in commercial genomic testing.
McGowan ML, Fishman JR, Settersten RA Jr, Lambrix MA, Juengst ET.
PLoS One. 2014 Sep 26;9(9):e108484.


STUB1 mutations in autosomal recessive ataxias; evidence for mutation-specific clinical heterogeneity.
Heimdal K, Sanchez-Guixé M, Aukrust I, Bollerslev J, et al.
Orphanet J Rare Dis. 2014 Sep 26;9(1):146.


RNA-sequencing reveals oligodendrocyte and neuronal transcripts in microglia relevant to central nervous system disease.
Solga AC, Pong WW, Walker J, Wylie T, et al.
Glia. 2014 Sep 24. [Epub ahead of print]


Confirmation of the cellular targets of benomyl and rapamycin using next-generation sequencing of resistant mutants in S. cerevisiae.
Wride DA, Pourmand N, Bray WM, Kosarchuk JJ, et al.
Mol Biosyst. 2014 Sep 26. [Epub ahead of print]


Clinical multiplexed exome sequencing distinguishes adult oligodendroglial neoplasms from astrocytic and mixed lineage gliomas.
Cryan JB, Haidar S, Ramkissoon LA, Bi WL, et al.
Oncotarget. 2014 Aug 12. [Epub ahead of print]


A balanced look at the implications of genomic (and other "omics") testing for disease diagnosis and clinical care.
Boyd SD, Galli SJ, Schrijver I, Zehnder JL, et al.
Genes. 2014 Sep 1;5(3):748-66.


The RBMX gene as a candidate for the Shashi X-linked intellectual disability syndrome (SMRXS).
Shashi V, Xie P, Schoch K, Goldstein DB, et al.
Clin Genet. 2014 Sep 26. [Epub ahead of print]


Discrepancies in cancer genomic sequencing highlight opportunities for driver mutation discovery.
Hudson AM, Yates T, Li Y, Trotter EW, et al.
Cancer Res. 2014 Sep 25. [Epub ahead of print]


Next generation DNA sequencing of a Swedish malignant hyperthermia cohort.
Broman M, Kleinschnitz I, Bach EJ, Rost S, et al.
Clin Genet. 2014 Sep 25. [Epub ahead of print]


Development of DNA confirmatory and high-risk diagnostic testing for newborns using targeted next-generation DNA sequencing.
Bhattacharjee A, Sokolsky T, Wyman SK, Reese MG, et al.
Genet Med. 2014 Sep 25. [Epub ahead of print]


Regulatory changes raise troubling questions for genomic testing.
Evans BJ, Dorschner MO, Burke W, Jarvik GP.
Genet Med. 2014 Sep 25. [Epub ahead of print]


Clinical laboratory response to a mock outbreak of invasive bacterial infections: a preparedness study.
Olsen RJ, Fittipaldi N, Kachroo P, Sanson MA, et al.
J Clin Microbiol. 2014 Sep 24. [Epub ahead of print]


KIF1A mutation in a patient with progressive neurodegeneration.
Okamoto N, Miya F, Tsunoda T, Yanagihara K, et al.
J Hum Genet. 2014 Sep 25. [Epub ahead of print]


Detecting novel genetic mutations in Chinese Usher syndrome families using next-generation sequencing technology.
Qu LH, Jin X, Xu HW, Li SY, Yin ZQ.
Mol Genet Genomics. 2014 Sep 25. [Epub ahead of print]


Clonal evolution revealed by whole genome sequencing in a case of primary myelofibrosis transformed to secondary acute myeloid leukemia.
Engle EK, Fisher DA, Miller CA, McLellan MD, et al.
Leukemia. 2014 Sep 25. [Epub ahead of print]


Screening for trisomies 21, 18 and 13 cell-free DNA analysis of maternal blood at 10-11 weeks' gestation and the combined test at 11-13 weeks.
Quezada MS, Del Mar Gil M, Francisco C, Oròsz G, Nicolaides KH.
Ultrasound Obstet Gynecol. 2014 Sep 24. [Epub ahead of print]


Intragenic duplication-A novel causative mechanism for SATB2-associated syndrome.
Liedén A, Kvarnung M, Nilssson D, Sahlin E, Lundberg ES.
Am J Med Genet A. 2014 Sep 23. [Epub ahead of print]


HIBCH deficiency in a patient with phenotypic characteristics of mitochondrial disorders.
Reuter MS, Sass JO, Leis T, Köhler J, et al.
Am J Med Genet A. 2014 Sep 23. [Epub ahead of print]


Identification of a novel missense mutation in the WFS1 gene as a cause of autosomal dominant nonsyndromic sensorineural hearing loss in all-frequencies.
Bai X, Lv H, Zhang F, Liu J, et al.
Am J Med Genet A. 2014 Sep 23. [Epub ahead of print]


Novel mutation in TSPAN12 leads to autosomal recessive inheritance of congenital vitreoretinal disease with intra-familial phenotypic variability.
Gal M, Levanon EY, Hujeirat Y, Khayat M, et al.
Am J Med Genet A. 2014 Sep 22. [Epub ahead of print]


Transmission of methicillin-resistant Staphylococcus aureus infection through solid organ transplantation: confirmation via whole genome sequencing.
Wendt JM, Kaul D, Limbago BM, Ramesh M, et al.
Am J Transplant. 2014 Sep 22. [Epub ahead of print]


Transmission of methicillin-resistant Staphylococcus aureus via deceased donor liver transplantation confirmed by whole genome sequencing.
Altman DR, Sebra R, Hand J, Attie O, et al.
Am J Transplant. 2014 Sep 22. [Epub ahead of print]


Leiomodin-3 dysfunction results in thin filament disorganization and nemaline myopathy.
Yuen M, Sandaradura SA, Dowling JJ, Kostyukova AS, et al.
J Clin Invest. 2014 Sep 24. [Epub ahead of print]


Identification of novel mutations by exome sequencing in African American colorectal cancer patients.
Ashktorab H, Daremipouran M, Devaney J, Varma S, et al.
Cancer. 2014 Sep 23. [Epub ahead of print]


Genetic profiling of thymic carcinoma using targeted next-generation sequencing.
Shitara M, Okuda K, Suzuki A, Tatematsu T, et al.
Lung Cancer. 2014 Sep 10. [Epub ahead of print]


Coffin-Siris and Nicolaides-Baraitser syndromes are a common well recognizable cause of intellectual disability.
Mari F, Marozza A, Mencarelli MA, Lo Rizzo C, et al.
Brain Dev. 2014 Sep 20. [Epub ahead of print]


Intratumor heterogeneity in hepatocellular carcinoma.
Friemel J, Rechsteiner MP, Frick L, Boehm F, et al.
Clin Cancer Res. 2014 Sep 23. [Epub ahead of print]


Haploinsufficiency of Dmxl2, encoding a synaptic protein, causes infertility associated with a loss of GnRH neurons in mouse.
Tata B, Huijbregts L, Jacquier S, Csaba Z, et al.
PLoS Biol. 2014 Sep 23;12(9):e1001952.


Spatial and temporal evolution of distal 10q deletion, a prognostically unfavorable event in diffuse low-grade gliomas.
van Thuijl HF, Scheinin I, Sie D, Alentorn A, et al.
Genome Biol. 2014 Sep 23;15(9):471.


Pure and syndromic optic atrophy explained by deep intronic OPA1 mutations and an intralocus modifier.
Bonifert T, Karle KN, Tonagel F, Batra M, et al.
Brain. 2014 Aug;137(Pt 8):2164-77.


Informed consent for exome sequencing research in families with genetic disease: The emerging issue of incidental findings.
Bergner AL, Bollinger J, Raraigh KS, Tichnell C, et al.
Am J Med Genet A. 2014 Sep 22. [Epub ahead of print]


Family-based association test using both common and rare variants and accounting for directions of effects for sequencing data.
Chung RH, Tsai WY, Martin ER.
PLoS One. 2014 Sep 22;9(9):e107800.


Functional analysis of variance for association studies.
Vsevolozhskaya OA, Zaykin DV, Greenwood MC, Wei C, Lu Q.
PLoS One. 2014 Sep 22;9(9):e105074.


Functional analysis of variance for association studies.
Vsevolozhskaya OA, Zaykin DV, Greenwood MC, Wei C, Lu Q.
PLoS One. 2014 Sep 22;9(9):e105074.


Deep sequencing reveals stepwise mutation acquisition in paroxysmal nocturnal hemoglobinuria.
Shen W, Clemente MJ, Hosono N, Yoshida K, et al.
J Clin Invest. 2014 Sep 17. [Epub ahead of print]


Mutations in ADAR1, IFIH1, and RNASEH2B presenting as spastic paraplegia.
Crow YJ, Zaki MS, Abdel-Hamid MS, Abdel-Salam G, et al.
Neuropediatrics. 2014 Sep 22. [Epub ahead of print]


Identification of I411K, a novel missense EYA4 mutation causing autosomal dominant non‑syndromic hearing loss.
Tan M, Shen X, Yao J, Wei Q, et al.
Int J Mol Med. 2014 Sep 19. [Epub ahead of print]


Single-cell RNA sequencing identifies extracellular matrix gene expression by pancreatic circulating tumor cells.
Ting DT, Wittner BS, Ligorio M, Vincent Jordan N, et al.
Cell Rep. 2014 Sep 25;8(6):1905-18.


Validation of multiple annealing and looping-based amplification cycle sequencing for 24-chromosome aneuploidy screening of cleavage-stage embryos.
Huang J, Yan L, Fan W, Zhao N, et al.
Fertil Steril. 2014 Sep 17. [Epub ahead of print]


Exome sequencing identifies a novel homozygous variant in NDRG4 in a family with infantile myofibromatosis.
Linhares ND, Freire MC, Cardenas RG, Pena HB, et al..
Eur J Med Genet. 2014 Sep 17. pii: S1769-7212(14)00171-2.


Novel pathogenic COL11A1/COL11A2 variants in Stickler syndrome detected by targeted NGS and exome sequencing.
Acke FR, Malfait F, Vanakker OM, Steyaert W, et al.
Genet Metab. 2014 Sep 8. [Epub ahead of print]


Identification of chimeric TSNAX-DISC1 resulting from intergenic splicing in endometrial carcinoma through high-throughput RNA sequencing.
Li N, Zheng J, Li H, Deng J, et al.
Carcinogenesis. 2014 Sep 19. [Epub ahead of print]


Genomic analysis of bone marrow failure and myelodysplastic syndromes reveals phenotypic and diagnostic complexity.
Zhang MY, Keel SB, Walsh T, Lee MK, et al.
Haematologica. 2014 Sep 19. [Epub ahead of print]


Characterization of a de novo SCN8A mutation in a patient with epileptic encephalopathy.
de Kovel CG, Meisler MH, Brilstra EH, van Berkestijn FM, et al.
Epilepsy Res. 2014 Sep 4. [Epub ahead of print]


Novel fusion transcripts associate with progressive prostate cancer.
Yu YP, Ding Y, Chen Z, Liu S, et al.
Am J Pathol. 2014 Sep 1. [Epub ahead of print]


High-throughput sequencing of plasma microRNA in chronic fatigue syndrome/myalgic encephalomyelitis.
Brenu EW, Ashton KJ, Batovska J, Staines DR, Marshall-Gradisnik SM.
PLoS One. 2014 Sep 19;9(9):e102783.


A serum microRNA panel as potential biomarkers for hepatocellular carcinoma related with hepatitis B virus.
Tan Y, Ge G, Pan T, Wen D, et al.
PLoS One. 2014 Sep 19;9(9):e107986.


Differential and limited expression of mutant alleles in multiple myeloma.
Rashid NU, Sperling AS, Bolli N, Wedge DC, et al.
Blood. 2014 Sep 18. [Epub ahead of print]


Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.
Merid SK, Goranskaya D, Alexeyenko A.
BMC Bioinformatics. 2014 Sep 19;15(1):308.


Progressive hyperpigmentation in a Taiwanese child due to an inborn error of vitamin B12 metabolism (cblJ).
Takeichi T, Hsu CK, Yang HS, Chen HY, et al.
Br J Dermatol. 2014 Sep 18. [Epub ahead of print]


Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype.
Zhang Y, Liu Y, Li Y, Duan Y, et al.
BMC Med Genet. 2014 Sep 19;15(1):105.


Transcriptome analysis of pancreatic cancer reveals a tumor suppressor function for HNF1A.
Hoskins JW, Jia J, Flandez M, Parikh H, et al.
Carcinogenesis. 2014 Sep 18. [Epub ahead of print]


Genomic analyses of gynaecologic carcinosarcomas reveal frequent mutations in chromatin remodelling genes.
Jones S, Stransky N, McCord CL, Cerami E, et al.
Nat Commun. 2014 Sep 19;5:5006.


Single point mutation in Rabenosyn-5 in a female with intractable seizures and evidence of defective endocytotic trafficking.
Stockler S, Corvera S, Lambright D, Fogarty K, et al.
Orphanet J Rare Dis. 2014 Sep 20;9(1):141.


'Hope for safe prenatal gene tests'. A content analysis of how the UK press media are reporting advances in non-invasive prenatal testing.
Lewis C, Choudhury M, Chitty LS.
Prenat Diagn. 2014 Sep 18. [Epub ahead of print]

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