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In Print: Last Week's Clinical Sequencing Papers of Note: May 1, 2013

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AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes.
Na YJ, Cho Y, Kim JH.
Healthc Inform Res. 2013 Mar;19(1):50-5.


A method to prioritize quantitative traits and individuals for sequencing in family-based studies.
Shah KP, Douglas JA.
PLoS One. 2013 Apr 23;8(4):e62545.


Employing MCMC under the PPL framework to analyze sequence data in large pedigrees.
Huang Y, Thomas A, Vieland VJ.
Front Genet. 2013 Apr 19;4:59.


Association Between Variants of PRDM1 and NDP52 and Crohns Disease, Based on Exome Sequencing and Functional Studies.
Ellinghaus D, Zhang H, Zeissig S, Lipinski S, et al.
Gastroenterology. 2013 Apr 25. pii: S0016-5085(13)00620-3. [Epub ahead of print]


Forty-five years to diagnosis.
Erdmann J, Schunkert H.
Neuromuscul Disord. 2013 Apr 25. [Epub ahead of print]


ZC4H2 Mutations Are Associated with Arthrogryposis Multiplex Congenita and Intellectual Disability through Impairment of Central and Peripheral Synaptic Plasticity.
Hirata H, Nanda I, van Riesen A, McMichael G, et al.
Am J Hum Genet. 2013 Apr 24. [Epub ahead of print]


Yunis-Varón Syndrome Is Caused by Mutations in FIG4 Encoding a Phosphoinositide Phosphatase.
Campeau PM, Lenk GM, Lu JT, Bae Y, et al.
Am J Hum Genet. 2013 Apr 23. [Epub ahead of print]


Mutations in ERCC4, Encoding the DNA-Repair Endonuclease XPF, Cause Fanconi Anemia.
Bogliolo M, Schuster B, Stoepker C, Derkunt B, et al.
Am J Hum Genet. 2013 Apr 23. [Epub ahead of print]


Punctuated evolution of prostate cancer genomes.
Baca SC, Prandi D, Lawrence MS, Mosquera JM, et al.
Cell. 2013 Apr 25;153(3):666-77.


Intellectual disability associated with a homozygous missense mutation in THOC6.
Beaulieu CL, Huang L, Innes AM, Akimenko MA, et al.
Orphanet J Rare Dis. 2013 Apr 26;8(1):62.


Variations in COL15A1 and COL18A1 influence age of onset of primary open angle glaucoma.
Wiggs JL, Howell GR, Linkroum K, Abdrabou W, et al.
Clin Genet. 2013 Apr 26. [Epub ahead of print]


Next-generation sequencing of cancer consensus genes in lymphoma.
Hüllein J, Jethwa A, Stolz T, Blume C, et al.
Leuk Lymphoma. 2013 Apr 29. [Epub ahead of print]


Clinical spectrum of early onset epileptic encephalopathies caused by KCNQ2 mutation.
Kato M, Yamagata T, Kubota M, Arai H, et al.
Epilepsia. 2013 Apr 26. [Epub ahead of print]


Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus.
Alazami AM, Hijazi H, Al-Dosari MS, Shaheen R, et al.
J Med Genet. 2013 Apr 25. [Epub ahead of print]


Genome sequencing of mucosal melanomas reveals that they are driven by distinct mechanisms from cutaneous melanoma.
Furney SJ, Turajlic S, Stamp G, Nohadani M, et al.
J Pathol. 2013 Apr 25. [Epub ahead of print]


A mosaic PTEN mutation causing Cowden syndrome identified by deep sequencing.
Pritchard CC, Smith C, Marushchak T, Koehler K, et al.
Genet Med. 2013 Apr 25. [Epub ahead of print]


Self-guided management of exome and whole-genome sequencing results: changing the results return model.
Yu JH, Jamal SM, Tabor HK, Bamshad MJ.
Genet Med. 2013 Apr 25. [Epub ahead of print]


ACMG position statement on prenatal/preconception expanded carrier screening.
Grody WW, Thompson BH, Gregg AR, Bean LH, et al.
Genet Med. 2013 Apr 25. [Epub ahead of print]


Frequent mutation of the PI3K pathway in head and neck cancer defines predictive biomarkers.
Lui VW, Hedberg ML, Li H, Vangara BS, et al.
Cancer Discov. 2013 Apr 25. [Epub ahead of print]


Deep ion sequencing of amplicon adapter ligated libraries: a novel tool in molecular diagnostics of formalin fixed and paraffin embedded tissues.
Becker K, Vollbrecht C, Koitzsch U, Koenig K, et al.
J Clin Pathol. 2013 Apr 25. [Epub ahead of print]


Transplantation-associated long-term immunosuppression promotes oral colonization by potentially opportunistic pathogens without impacting other members of the salivary bacteriome.
Diaz PI, Hong BY, Frias-Lopez J, Dupuy AK, et al.
Clin Vaccine Immunol. 2013 Apr 24. [Epub ahead of print]


Complete Genomic Landscape of a Recurring Sporadic Parathyroid Carcinoma.
Kasaian K, Wiseman SM, Thiessen N, Mungall KL, et al.
J Pathol. 2013 Apr 24. [Epub ahead of print]


Whole-exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity.
Gill R, Him Cheung Y, Shen Y, Lanzano P, et al.
Obesity (Silver Spring). 2013 Apr 24. [Epub ahead of print]


Gene fusions by chromothripsis of chromosome 5q in the VCaP prostate cancer cell line.
Teles Alves I, Hiltemann S, Hartjes T, van der Spek P, et al.
Hum Genet. 2013 Apr 25. [Epub ahead of print]


Loss of function of KIAA2022 causes mild to severe intellectual disability with an autism spectrum disorder and impairs neurite outgrowth.
Van Maldergem L, Hou Q, Kalscheuer VM, Rio M, et al.
Hum Mol Genet. 2013 Apr 24. [Epub ahead of print]


Extended haplotype association study in Crohn's disease identifies a novel, Ashkenazi Jewish-specific missense mutation in the NF-κB pathway gene, HEATR3.
Zhang W, Hui KY, Gusev A, Warner N, et al.
Genes Immun. 2013 Apr 25. [Epub ahead of print]


A Frameshift Mutation in the Cubilin Gene (CUBN) in Border Collies with Imerslund-Gräsbeck Syndrome (Selective Cobalamin Malabsorption).
Owczarek-Lipska M, Jagannathan V, Drögemüller C, Lutz S, et al.
PLoS One. 2013 Apr 16;8(4):e61144.


Noninvasive prenatal molecular karyotyping from maternal plasma.
Yu SC, Jiang P, Choy KW, Chan KC, et al.
PLoS One. 2013 Apr 17;8(4):e60968.


Identification of hepatotropic viruses from plasma using deep sequencing: a next generation diagnostic tool.
Law J, Jovel J, Patterson J, Ford G, et al.
PLoS One. 2013 Apr 17;8(4):e60595.


Genetic risk prediction for normal-karyotype acute myeloid leukemia using whole-exome sequencing.
Heo SG, Hong EP, Park JW.
Genomics Inform. 2013 Mar;11(1):46-51.


Annotation of genes having candidate somatic mutations in acute myeloid leukemia with whole-exome sequencing using concept lattice analysis.
Lee KH, Lim JH, Kim JH.
Genomics Inform. 2013 Mar;11(1):38-45.


Bioinformatics interpretation of exome sequencing: blood cancer.
Kim J, Lee YG, Kim N.
Genomics Inform. 2013 Mar;11(1):24-33.


Massively parallel sequencing, ArrayCGH and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.
Chandrasekharappa SC, Lach FP, Kimble DC, Kamat A, et al.
Blood. 2013 Apr 23. [Epub ahead of print]


Validation of targeted sequencing of single-nucleotide polymorphisms for non-invasive prenatal detection of aneuploidy of chromosomes 13, 18, 21, X, and Y.
Nicolaides KH, Syngelaki A, Gil M, Atanasova V, Markova D.
Prenat Diagn. 2013 Apr 24:1-5. [Epub ahead of print]


Characterization and Identification of Novel Serum miRNAs in Sepsis Patients With Different Outcomes.
Wang HJ, Zhang PJ, Chen WJ, Jie D, et al.
Shock. 2013 Apr 22. [Epub ahead of print]


Attitudes of african americans toward return of results from exome and whole genome sequencing.
Yu JH, Crouch J, Jamal SM, Tabor HK, Bamshad MJ .
Am J Med Genet A. 2013 May;161(5):1064-72.


Practices and policies of clinical exome sequencing providers: analysis and implications.
Jamal SM, Yu JH, Chong JX, Dent KM, et al.
Am J Med Genet A. 2013 May;161(5):935-50.


Whole-exome sequencing and imaging genetics identify functional variants for rate of change in hippocampal volume in mild cognitive impairment.
Nho K, Corneveaux JJ, Kim S, Lin H, et al.
Mol Psychiatry. 2013 Apr 23. [Epub ahead of print]


Understanding barriers to Borrelia burgdorferi dissemination during infection using massively parallel sequencing.
Troy EB, Lin T, Gao L, Lazinski DW, et al.
Infect Immun. 2013 Apr 22. [Epub ahead of print]


Hereditary myopathy with early respiratory failure: occurrence in various populations.
Palmio J, Evilä A, Chapon F, Tasca G, et al.
J Neurol Neurosurg Psychiatry. 2013 Apr 19. [Epub ahead of print]


A novel syndrome of hypohidrosis and intellectual disability is linked to COG6 deficiency.
Shaheen R, Ansari S, Alshammari MJ, Alkhalidi H, et al.
J Med Genet. 2013 Apr 20. [Epub ahead of print]


Rheumatoid arthritis synovial tissue harbours dominant B-cell and plasma-cell clones associated with autoreactivity.
Doorenspleet ME, Klarenbeek PL, de Hair MJ, van Schaik BD, et al.
Ann Rheum Dis. 2013 Apr 20. [Epub ahead of print]


Cytoplasmic Mislocalization of POU3F4 Due to Novel Mutations Leads to Deafness in Humans and Mice.
Parzefall T, Shivatzki S, Lenz DR, Rathkolb B, et al.
Hum Mutat. 2013 Apr 18. [Epub ahead of print]


High throughput sequencing of IL23R reveals a low-frequency non-synonymous SNP that is associated with Ankylosing spondylitis in a Han Chinese population.
Davidson SI, Jiang L, Cortes A, Wu X, et al.
Arthritis Rheum. 2013 Apr 18. [Epub ahead of print]


RNA sequencing of cancer reveals novel splicing alterations.
Eswaran J, Horvath A, Godbole S, Reddy SD, et al.
Sci Rep. 2013 Apr 22;3:1689.


Whole exome sequencing in adult ETP-ALL reveals a high rate of DNMT3A mutations.
Neumann M, Heesch S, Schlee C, Schwartz S, et al.
Blood. 2013 Apr 19. [Epub ahead of print]


High-Resolution Profiling of Fetal DNA Clearance from Maternal Plasma by Massively Parallel Sequencing.
Yu SC, Lee SW, Jiang P, Leung TY, et al.
Clin Chem. 2013 Apr 19. [Epub ahead of print]


Clinical genomics information management software linking cancer genome sequence and clinical decisions.
Watt S, Jiao W, Brown AM, Petrocelli T, et al.
Genomics. 2013 Apr 17. [Epub ahead of print]


Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis.
Destefano GM, Fantauzzo KA, Petukhova L, Kurban M, et al.
Proc Natl Acad Sci U S A. 2013 Apr 19. [Epub ahead of print]


Peripheral blood transcriptome sequencing reveals rejection-relevant genes in long-term heart transplantation.
Chen Y, Zhang H, Xiao X, Jia Y, et al.
Int J Cardiol. 2013 Apr 18. [Epub ahead of print]


Personalised medicine in the genome era.
Chalmers D, Nicol D, Otlowski M, Critchley C.
J Law Med. 2013 Mar;20(3):577-94.


A complex V ATP5A1 defect causes fatal neonatal mitochondrial encephalopathy.
Jonckheere AI, Renkema GH, Bras M, van den Heuvel LP, et al.
Brain. 2013 Apr 18. [Epub ahead of print]


Using Ultradeep Pyrosequencing to Study HIV-1 Co-receptor Usage in Primary and Dual Infection.
Wagner GA, Pacold ME, Vigil E, Caballero G, et al.
J Infect Dis. 2013 Apr 18. [Epub ahead of print]


The Thr224Asn mutation in the VPS45 gene is associated with congenital neutropenia and primary myelofibrosis of infancy.
Stepensky P, Saada A, Cowan M, Tabib A, et al.
Blood. 2013 Apr 18. [Epub ahead of print]


Desktop Transcriptome Sequencing From Archival Tissue to Identify Clinically Relevant Translocations.
Sweeney RT, Zhang B, Zhu SX, Varma S, et al.
Am J Surg Pathol. 2013 Apr 16. [Epub ahead of print]


Lack of C9ORF72 coding mutations supports a gain of function for repeat expansions in amyotrophic lateral sclerosis.
Harms MB, Cady J, Zaidman C, Cooper P, et al.
Neurobiol Aging. 2013 Apr 16. [Epub ahead of print]


Whole-genome sequencing in an autism multiplex family.
Shi L, Zhang X, Golhar R, Otieno FG, et al.
Mol Autism. 2013 Apr 18;4(1):8.

The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.