25 May 2011:: SVA is published in Bioinformatics.

21 Mar 2011:: SVA V1.10 is released: [1]Supports GRCh build 37/hg19; [2] Supports user annotation track in GFF3 or BED formats.

9 Sep 2010:: The characterization of twenty sequenced human genomes. [Article]

12 Jul 2010:: LabCorp Launches Interleukin 28B Polymorphism (IL28B) Genotype Test to Support Individualized Treatment Decisions for Patients with Hepatitis C Viral Infection.

17 Jun 2010:: Causal variants for metachondromatosis are identified.
[Article] [SVA screenshot]
[GenomeWeb: The Daily Scan]

18 Mar 2010:: SVA 1.02[beta] is released.

11 Mar 2010:: SVA 1.01[beta] is released with a command line tool.

8 Mar 2010:: A lite evaluation edition is released for Windows. Play with it on your laptop!

23 Jan 2010:: SVA 1.00[beta] is released.

Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

Sobreira NLM, Cirulli ET, Avramopoulos D, Wohler E, Oswald GL, et al. (2010) PLoS Genet 6(6): e1000991. doi:10.1371/journal.pgen.1000991


Although more than 2,400 genes have been shown to contain variants that cause Mendelian disease, there are still several thousand such diseases yet to be molecularly defined. The ability of new whole-genome sequencing technologies to rapidly indentify most of the genetic variants in any given genome opens an exciting opportunity to identify these disease genes. Here we sequenced the whole genome of a single patient with the dominant Mendelian disease, metachondromatosis (OMIM 156250), and used partial linkage data from her small family to focus our search for the responsible variant. In the proband, we identified an 11 bp deletion in exon four of PTPN11 , which alters frame, results in premature translation termination, and co-segregates with the phenotype. In a second metachondromatosis family, we confirmed our result by identifying a nonsense mutation in exon 4 of PTPN11 that also co-segregates with the phenotype. Sequencing PTPN11 exon 4 in 469 controls showed no such protein truncating variants, supporting the pathogenicity of these two mutations. This combination of a new technology and a classical genetic approach provides a powerful strategy to discover the genes responsible for unexplained Mendelian disorders.


Full article on PLoSGenetics.org...