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

Infinium 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-24 v2

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 (716 845-4012)  or Prashant Singh (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.