Genotyping
News
The PCPGM High Throughput Sequenom and Illumina Genotyping service is now offering as a research tool, a panel of point mutations and insertion/deletions in EGFR, K-ras, B-raf, PIK3CA and ERBB2 that are commonly seen in non-small cell lung cancer. Analysis using this set of assays can be used in the assessment of prognosis and choice of therapy for non-small cell lung cancer. The panel was developed by Dr Pasi Janne at the Dana-Farber/Harvard Cancer CenterThe Power of SNPs
Single nucleotide polymorphisms (SNPs, pronounced snips) are the most common type of genetic variation in the human genome. Any two individuals are predicted to vary at more than a million different SNPs scattered throughout the genome. A small fraction of this genetic variation is likely to explain the majority of the differences between individuals, including their predisposition to development of many common human diseases, such as cardiovascular disease, hypertension, diabetes, asthma, and cancer. The Partners Genotyping Facility is designed to assist investigators in assessing this rich genetic variation in patient populations.
Project Design
The Human Genetics Research Service, is a collaborative effort between the Partners HealthCare Center for Personalized Genetic Medicine (PCPGM) and the Brigham and Women’s Center for Clinical Investigation (CCI). This program is designed to provide consultation to investigators regarding the incorporation of genetics and genomics in their research, including help in arranging collaborations and accessing available resources for genotyping, sequencing and genetic epidemiology.
View a video about the Genotyping Facility and SNPs:
Genotyping: Discovering the Individual
Introduction
The genotyping facility employs state of the art equipment, including Biomek and Multimek robotic pipetting devices, a 384 well ABI 7900 Taqman machine, a chip spotting device, a Sequenom mass spectrometry system and an Illumina BeadStation. This high-tech equipment forms the core of the genotyping facility and enables throughputs in excess of 100,000 SNP genotypes per day.
- The Partners Genotyping Facility
The Partners Genotyping Facility, part of the Partners HealthCare Center for Personalized Genetic Medicine, provides flexible, high quality, high throughput SNP genotyping to the Harvard Partners research community, including Harvard Medical School, hospitals in the Partners Healthcare network, investigators in the Dana Farber / Harvard Cancer Center, and the Harvard School of Public Health. The portfolio of Genotyping methods at PCPGM now includes Affymetrix, Illumina, Sequenom, TaqMan and TaqMan OpenArrays.
TaqMan SNP allelic discrimination is performed on the ABI7900. In this method, specialized probe oligonucleotides are used to distinguish the SNPs during or at the end of a PCR reaction. Depending upon a number of factors, including previous implementation of the method for a particular SNP, this method will be the first approach for genotyping in some cases.
TaqMan OpenArray (formerly Biotrove) genotyping is a nanofluidic chip based platform that allows us to run assays that we know work well using traditional 384- well format TaqMan assays. The OpenArray system allows users to run 16, 32 or 64 SNPs on one OpenArray. Depending on the number of SNPs on an OpenArray up to 144 samples can be run per OpenArray (in a 16-plex assay).
Sequenom genotyping is suitable for small numbers of SNPs, from 2 to 300 SNPs. It is performed using MALDI-TOF (Matrix-assisted laser desorption ionization – time of flight) mass spectrometry. Our service includes primer and assay design through to production of genotypes. All steps involved are highly automated and are tracked using a laboratory management system with bar coding. An average of 34 SNPs can be plexed into a single well of a 384 well plate using Sequenom iPLEX chemistry, with a maximum of 40 SNPs per plex. Specialized equipment for this work includes a Biomek multi-pipettor robot, a Multimek multi-pipettor robot, a nanoliter plotting robot for spotting the extension products onto chips, and the mass spectrometer.
Affymetrix Whole Genome Genotyping using the SNP chip is carried out by the PCPGM Microarray core. Click here to be directed to the PCPGM Microarray website.
The Illumina Bead Station GoldenGate assay system for SNP genotyping is a platform most suitable for researchers engaged in large scale association studies: whole genome linkage mapping panels and large scale fine mapping panels. The genotyping is carried out in 384 plex reactions then in multiples of 96 SNPs up to 1536 SNPs using Illumina custom SNP panels. Many standard panels are also available from Illumina.
The Illumina Bead Station Infinium assay system is also available for Whole Genome Genotyping. Genotyping is carried out on standard chips containing up to 1 million SNPs. Custom genotyping of large numbers of SNPs is also available using the iSelect system. Several standard chips allow the addition of iSelect custom SNP sets to allow customization of the chip for the researchers specific aims.
The facility can also perform custom fragment analysis genotyping for users who wish to use microsatellites, VNTR’s and insertion deletion polymorphisms in their research.