SNP Genotyping

Single nucleotide polymorphisms (SNPs) 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. A SNP is of greatest value for genetic mapping studies when both alleles have a frequency greater than ~20%. Some SNPs reside in open reading frames and lead to alternate amino acid sequences while others residing in regulatory regions may affect control.

Introduction

For high throughput SNP genotyping services, Life Sciences Technology Laboratory utilizes (LSTL) the resources available through AMDeC organization. We utilize the Sequenom MassARRAY Compact system to offer high-performance DNA analysis. This platform efficiently and precisely measures the amount of genetic target material and variations using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and is able to deliver reliable and specific data from complex biological samples and from trace amounts of genetic target material. The MassARRAY Compact system supports virtually all customer DNA analysis needs, including:

  • High-Performance SNP Genotyping
  • Targeted SNP Discovery
  • Allele Frequency Analysis
  • Gene Expression Analysis
  • Long-Range Haplotyping
  • Methylation Studies
  • Copy Number Verification

All applications are supported by SEQUENOM’s available hardware, software and proprietary SpectroCHIP consumables, which automatically generates analysis data and assigns a status level to samples.

The Life Sciences Technology Laboratory utilizes the resources available to us through AMDeC. These services include the state of the art equipment including Qiagen and Tecan robotic pippetting devices, 4 x 384 well PTC-225 thermalcycling machines, a Samsung chip spotting device, and the MassARRAY compact system for determining the absolute mass of short DNA sequences. This high-tech equipment forms the core of the genotyping facility and enables throughputs in excess of 10,000 SNP genotypes per day.

High Density SNP Array

GeneChip® Mapping Arrays enable The Mount Sinai Health System’s affiliated researchers to conduct large-scale linkage analysis, association, and copy number studies at a greater throughput and at a lower cost per data point. These high-density arrays contain thousands of single nucleotide polymorphisms (SNPs), and easy-to-use assays require only a single primer.

Each SNP on a GeneChip Mapping Array is interrogated with approximately 40 different probes, enabling GeneChip® Software to make highly accurate, automated genotype calls. With capability to process high density GeneChip Mapping Arrays, Life Sciences Technology Laboratory is bringing whole-genome analysis to the benchtop and enabling researchers to perform experiments in days that previously required weeks or months.

The Life Sciences Technology laboratory offers a suite of SNP genotyping platforms.

Whole Genome Human Mapping Arrays

The high density human mapping arrays listed below are used for association studies, linkage analysis, and copy number studies.

  • Affymetrix 10K human mapping arrays
  • Affymetrix 50K human mapping arrays
  • Affymetrix 250K human mapping arrays
  • Affymetrix 500K human mapping arrays (coming soon)

Please contact Greg Khitrov to discuss your high throughput genotyping project.