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Clinical Sequencing Papers of the Last Two Weeks


Whole transcriptome sequencing reveals recurrent NOTCH1 mutations in mantle cell lymphoma.
Kridel R, Meissner B, Rogic S, Boyle M, et al.
Blood. 2011 Dec 30. [Epub ahead of print]

Rapid genomic-scale analysis of Escherichia coli O104:H4 using high-resolution alternative methods to next generation sequencing.
Jackson SA, Kotewicz ML, Patel IR, Lacher DW, et al.
Appl Environ Microbiol. 2011 Dec 30. [Epub ahead of print]

Design and analytical validation of clinical DNA sequencing assays.
Pont-Kingdon G, Gedge F, Wooderchak-Donahue W, Schrijver I, et al.
Arch Pathol Lab Med. 2012 Jan;136(1):41-6.

Targeted next-generation sequencing in anophthalmia and microphthalmia patients confirms SOX2, OTX2 and FOXE3 mutations.
Lopezjimenez N, Flannick J, Yahyavi M, Li J, et al.
BMC Med Genet. 2011 Dec 28;12(1):172.

Use of Illumina deep sequencing technology to differentiate hepatitis C virus variants.
Ninomiya M, Ueno Y, Funayama R, Nagashima T, et al.
Clin Microbiol. 2011 Dec 28. [Epub ahead of print]

Expressed antibody repertoires in human cord blood cells: 454 sequencing and IMGT/HighV-QUEST analysis of germline gene usage, junctional diversity, and somatic mutations.
Prabakaran P, Chen W, Singarayan MG, Stewart CC, et al.
Immunogenetics. 2011 Dec 27. [Epub ahead of print]

Mutations in the colony stimulating factor 1 receptor (CSF1R) gene cause hereditary diffuse leukoencephalopathy with spheroids.
Rademakers R, Baker M, Nicholson AM, Rutherford NJ, et al.
Nat Genet. 2011 Dec 25. [Epub ahead of print]

Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.
Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, et al.
Nat Genet. 2011 Dec 25. [Epub ahead of print]

Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing.
Stark MS, Woods SL, Gartside MG, Bonazzi VF, et al.
Nat Genet. 2011 Dec 25. [Epub ahead of print]

Exome sequence identifies RIPK4 as the Bartsocas-Papas syndrome locus.
Mitchell K, O'Sullivan J, Missero C, Blair E, et al.
Am J Hum Genet. 2011 Dec 20. [Epub ahead of print]

Exome sequencing identifies SLCO2A1 mutations as a cause of primary hypertrophic osteoarthropathy.
Zhang Z, Xia W, He J, Zhang Z, et al.
Am J Hum Genet. 2011 Dec 20. [Epub ahead of print]

The origins of African Plasmodium vivax; insights from mitochondrial genome sequencing.
Culleton R, Coban C, Zeyrek FY, Cravo P, et al.
PLoS One. 2011;6(12):e29137.

Serum MicroRNA expression profile as a biomarker in the diagnosis and prognosis of pancreatic cancer.
Liu R, Chen X, Du Y, Yao W, et al.
Clin Chem. 2011 Dec 22. [Epub ahead of print]

COLD-PCR enrichment of rare cancer mutations prior to targeted amplicon resequencing.
Milbury CA, Correll M, Quackenbush J, Rubio R, Makrigiorgos GM.
Clin Chem. 2011 Dec 21. [Epub ahead of print]

Fusion of KIF5B and RET transforming gene in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing.
Ju YS, Lee WC, Shin JY, Lee S, et al.
Genome Res. 2011 Dec 22. [Epub ahead of print]

Whole genome sequencing of matched primary and metastatic acral melanomas.
Turajlic S, Furney SJ, Lambros MB, Mitsopoulos C, et al.
Genome Res. 2011 Dec 19. [Epub ahead of print]

Germline mutations in the oncogene EZH2 cause Weaver syndrome and increased human height.
Tatton-Brown K, Hanks S, Ruark E, Zachariou A, et al.
Oncotarget. 2011 Dec 21. [Epub ahead of print]

Rare variants in the CYP27B1 gene are associated with multiple sclerosis.
Ramagopalan SV, Dyment DA, Cader MZ, Morrison KM, et al.
Ann Neurol. 2011 Dec;70(6):881-6.

Frequent deletions of JARID2 in leukemic transformation of chronic myeloid malignancies.
Puda A, Milosevic JD, Berg T, Klampfl T, et al.
Am J Hematol. 2011 Nov 18. [Epub ahead of print]

Recurrent somatic DICER1 mutations in nonepithelial ovarian cancers.
Heravi-Moussavi A, Anglesio MS, Cheng SW, Senz J, et al.
N Engl J Med. 2011 Dec 21. [Epub ahead of print]

Analysis of cancer metabolism with high-throughput technologies.
Markovets AA, Herman D.
BMC Bioinformatics. 2011 Oct 18;12 Suppl 10:S8.

The Scan

Study Points to Tuberculosis Protection by Gaucher Disease Mutation

A mutation linked to Gaucher disease in the Ashkenazi Jewish population appears to boost Mycobacterium tuberculosis resistance in a zebrafish model of the lysosomal storage condition, a new PNAS study finds.

SpliceVault Portal Provides Look at RNA Splicing Changes Linked to Genetic Variants

The portal, described in Nature Genetics, houses variant-related messenger RNA splicing insights drawn from RNA sequencing data in nearly 335,700 samples — a set known as the 300K-RNA resource.

Automated Sequencing Pipeline Appears to Allow Rapid SARS-CoV-2 Lineage Detection in Nevada Study

Researchers in the Journal of Molecular Diagnostics describe and assess a Clear Labs Dx automated workflow, sequencing, and bioinformatic analysis method for quickly identifying SARS-CoV-2 lineages.

UK Team Presents Genetic, Epigenetic Sequencing Method

Using enzymatic DNA preparation steps, researchers in Nature Biotechnology develop a strategy for sequencing DNA, along with 5-methylcytosine and 5-hydroxymethylcytosine, on existing sequencers.