Partners Research Cores| HPCGG DNA Sequencing Core

News: The HPCGG High Throughput Sequencing Facility has recently added two Illumina Genome Analyzers, and we are happy to make the Solexa sequencing technology available to our clients. Please contact us about how projects may be developed to take advantage of this next generation sequencing capability.

The Sequencing Group currently supports two sequencing platforms: ABI 3730xl Analyzers for fluorescence-based DNA sequencing and cycle sequencing with di-deoxynucleotide terminator chemistry, and Illumina Genome Analyzers , employing the Solexa sequencing technology.

The DNA Sequencing Group at the Harvard Partners Center for Genetics and Genomics has a strong history of producing high quality, dependable and informative results for collaborators and clients. We participated in the Human Genome Project, building the STS-Based BAC map for Human Chromosome 12 (1), and providing Chromosome 12 tiling path clones to the Baylor Human Genome Sequencing Center for sequencing(2). We sequenced 113 BACs for the Mouse Genome Project, contributing 24 megabases of finished mouse sequence to the published Mouse Genome(3). We have provided draft sequences for unique strains of several bacterial genomes, including Pseudomonas aeruginosa(4), and Vibrio cholerae(5). More recently, we have participated in identifying mutations linked to numerous diseases, either in collaborations(6) or by providing client laboratories with full service resequencing and analysis(7).

Montgomery KT, Lee E, Miller A, Lau S, Shim C, Decker J, Chiu D, Emerling S, Sekhon M, Kim R, Lenz J, Han J, Ioshikhes I, Renault B, Marondel I, Yoon S-J K, Song K, Murty VVVS, Scherer S, Yonescu R, Kirsch IR, Ried T, McPherson J, Gibbs R, Kucherlapati R. A high-resolution map of human chromosome 12. Nature 2001;409:945-946.
Scherer, S., R. Kucherlapati, K. Montgomery, L. Li, Nelson D, Kucherlapati R, Weinstock G, Gibbs RA et al.; Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team. The finished DNA sequence of human chromosome 12. Nature 2006; 440:346-351.
Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, et al.; Mouse Genome Sequencing Consortium. Initial sequencing and comparitive analysis of the mouse genome. Nature 2002; 420:520-562.
Lee DG, Urbach JM, Wu G, Liberati NT, Feinbaum RL, Miyata S, Diggins LT, He J, Saucier M, Deziel E, Friedman L, Li L, Grills G, Montgomery K, Kucherlapati R, Rahme LG, Ausubel FM. Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatrorial. Genome Biol. 2006;7(10):R90.
Dziejman M, Serruto D, Tam VC, Sturtevant D, Diraphat P, Faruque SM, Rahman MH, Heidelberg JF, Decker J, Li L, Montgomery KT, Grills G, Kucherlapati R, Mekalanos JJ. Genomic characterization of non-O1, non-O139 Vibrio cholerae reveals genes for a type III secretion system. Proc Natl Acad Sci U S A. 2005 Mar 1;102(9):3465-70. Epub 2005 Feb 22
Roberts, AE, Araki T, Swanson KD, Montgomery, KT, Schiripo TA, Joshi VA, Li L, Yassin Y, Tamburino AM, Neel BG, Kucherlapati R. Germline gain-of-function mutations in SOS1 cause Noonan syndrome. Nat Genet. 2007 Jan;39(1):70-4.
Siepka SM, Yoo S-H, Park J, Song W, Kumar V, Hu Y, Lee C, Takahashi JS. Circadian Mutant Overtime Reveals F-box Protein FBXL3 Regulation of Cryptochrome and Period Gene Expression. Cell. 2007; 129:1011-1023.

Director: Oleg Iartchouk, Ph.D.
Phone: (617) 768-8377
Email: oiartchouk@partners.org

Other Staff:

Research Assistant: Stephanie Jeanne Loomis
Phone: (617) 768-8435
Email: sjloomis@partners.org

Research Assistant: Vanessa Obourn
Phone: (617) 768-8445
Email: vsobourn@partners.org

Research Assistant: Landon Merrill
Phone: (617) 768-8430
Email: lmerrill1@partners.org

Bioinformatician: Dmitriy Sonkin
Phone: (617) 768-8431
Email: dsonkin@partners.org

Instructor in Medicine: Kate Montgomery, Ph.D.
Consultant, Library Production and Informatics
Email: kmontgomery@rics.bwh.harvard.edu

We provide full-service resequencing of regions of interest in one or more genomic DNAs, including the following:

Discussion of the scope of the project and a cost quote
Identification of genes in the region of interest as needed, with the Investigator
Primer design using our automated system, to amplify desired regions
Primer ordering
QC of the primers on DNA standards, if required
PCR amplification of DNA provided by Investigator
PCR clean-up
Sequencing reactions
Sequencing reaction clean-up
Sequence application to the ABI 3730 XL Analyzer
Chromatograms are made available to Investigator over web (GIGPAD)
Data assembly and analysis using Phred Phrap and PolyPhred
One round of repeats and redesign if necessary
Report of variations found throughout sequence
Trouble shooting for 100% coverage if desired