SVA project

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25 Jan 2012:: We now have a new download site: www.OmicsExpress.com

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.

SVA in action

Screenshot 1: SVA genome browser shows a frameshifting coding INDEL (insertion/deletion) in the Factor VIII (F8) gene on chromosome X. This coding variant causes the type A hemophilia in one of the sequenced patients.

Screenshot 2: SVA Single Nucleotide Variant (SNV) list shows a premature stop SNV (stop-gained) in the Factor VIII (F8) gene on chromosome X. This coding variant causes the type A hemophilia in one of the sequenced patients.

(The red highlighting arrow was later added to this screenshot.)

Screenshot 3: SVA Insertion/Deletion (INDEL) list shows diverse frameshifting coding INDELs in the Factor VIII (F8) gene on chromosome X. Each of these distinct INDELs are carried by 1 or 2 patients, and cause the type A hemophilia.

(The red highlighting arrow was later added to this screenshot.)

Screenshot 4: SVA structural variation (SV) list shows a number of predicted deletions covering the whole length of some gene transcripts. These genes are usually pseudo-genes and/or these "functional" SVs are usually heterozygous (with only one strand of DNA deleted).

Screenshot 5: SVA variant density view shows the density of genetic variants identified.

Screenshot 6: SVA Gene Prioritization (SVA-GP) function ranks the Factor VIII (F8) gene as the first "possible candidate hit", by comparing 10 patient genomes with 10 control genomes.

The 10 patients are type A hemophilia patients resistant to HIV infection. This project is funded by the The Bill & Melinda Gates Foundation to David Goldstein at Duke University Institute for Genome Sciences & Policy (IGSP), Center for Human Genome Variation.

(Some pre-published data were manually masked in this screenshot.)

Screenshot 7: SVA gene biotype filter.

Screenshot 8: SVA biological pathway filter.

Screenshot 9: SVA OMIM disorder filter.

Screenshot 10: SVA gene filter.

Screenshot 11: SVA variant quality score filter.

Screenshot 12: SVA summary functions (under development).

Screenshot 13: SVA analysis functions (under development).

Screenshot 14: Another shot at SVA genome browser.