DNA CNV and LOH

The GSR provides DNA copy number variation (CNV), loss of heterozygosity (LOH) and global genotyping analyses on several different microarray platforms depending on the organism, starting material and size of your project.

  • Genotyping, CNV and LOH - Illumina BeadChips and Agilent Microarrays

Illumina BeadChips

The Infinium HD products include the HumanCytoSNP-12 and the Omni family of BeadChips. The Illumina BeadChips provide a broad spectrum of whole-genome DNA Analysis products to support a variety of experimental designs. Researchers have the flexibility to use panels of 300,000 to nearly 5,000,000 markers per sample, depending on their study goals. All of these BeadChips provide powerful and integrated genome-wide SNP genotyping, LOH and CNV detection.

BeadChip Number of Markers Minimum Kit Size
Infinium Core-24 307k 48
Infinium CoreExome-24 552k 48
Infinuim OmniExpress-24 714k 48
Infinium OmniExpressExome-8 961k 16
Infinium OmniZhongHua-8 878k 16
Infinium Multi-Ethnic Global-8 1748k 16
Infinium Multi-Ethnic AMR/AFR-8 1430k 16
Infinium Multi-Ethnic EUR/EAS/SAS-8 1475k 16
Infinium Omni2.5-8 2373k 16
Infinium Omni2.5Exome-8 2612k 16
Infinium Omni5-4 4284k 16
Infinium Omni5Exome-4 4549k 16
Infinium Exome-24 243k 48
Infinium ImmunoArray-24v2 254k 48
Infinium OncoArray-500k 499k 48
Infinium PsychArray-24 589k 48
Infinium QC Array-24 16k 48

NanoString Copy Number:

NanoString copy number variation analysis with nCounter. Ability to validate CNV studies in a simple cost effective way. Digital detection of target molecules and high level of multiplexing produce high sensitivity and reproducibility. NanoString uses barcodes and single-molecule imaging to detect hundreds of unique transcripts in a single reaction without amplification steps.

DNA Requirements – 0.2 - 2ug

Most standard genomic DNA isolation protocols will yield DNA of high enough purity for whole genome CN and LOH analysis. It is highly recommended to check genomic DNA for degradation and RNA contamination. It is critical to use purified and accurate amounts of DNA for fluorescent labeling. Please contact Sean Glenn at 716 845-4012 or Prashant Singh at 716 845-3869 for more details.

Core Grant Citation

This shared resource is funded by NCI P30CA16056. Publications should cite the Core grant in the acknowledgment section, if publications use data generated by the shared resource. Two copies of the publication acknowledging the Core grant should also be submitted to the facility at Elm & Carlton Streets, Buffalo, NY 14263.