Sequencing Products
CIDR offers a variety of Sequencing Products. Specifics are listed below.
| Product | Library Prep | Capture | Sequencer | Data Generation Target |
|---|---|---|---|---|
| Whole Genome Long Read | PCR Free size selected >25kb | NA | PromethION | Average of 25-30X, N50 ~30kb, whole genome methylation calls included |
| Whole Genome Short Read | PCR and PCR Free with double-sided SPRI clean-up | NA | NovaSeqXPlus | Average of 30X coverage with >99% concordance |
| Whole Exome | Low-Input | CIDR Custom Exome* | NovaSeqXPlus | Coverage of
|
| Custom Targeted | Low-Input | Custom design from: Twist,
IDT, Amplicon platforms |
NovaSeqXPlus | Coverage of
|
| Genotyping by Sequencing – low pass whole genome | Low-Input | N/A | NovaSeqXPlus | Coverage of
|
* CIDR Custom Exome is a Twist custom product that includes additional clinically relevant regions based on RefSeq and OMIM as well as Mitochondrial capture.
Genotyping by Sequencing
Two recent developments allow the utilization of low pass human whole genome sequencing (lpWGS) data for “genotyping by sequencing”. Imputation methods have been developed which optimize the speed and accuracy of genotype estimation using low-pass whole genome sequencing (lpWGS) and library preparation assays are available at much higher throughput and lower cost. Compared to SNP arrays with pre-selected variant sites which often target specific populations, lpWGS is unbiased in terms of variant sites, limited only by the sites observed in increasingly comprehensive population reference panels. Indeed, studies have shown that lpWGS can increase the power of GWAS1 and has more advantages than arrays in non-European populations2. The emergence of both new reference panels derived from large-scale diverse deep whole genome sequencing (WGS) data and more computationally efficient algorithms designed for imputation and phasing of lpWGS is now making lpWGS possible as a better alternative for SNP arrays1, 3, 4
CIDR has completed a pilot study to validate the practical implementation of this “Genotyping by Sequencing” service, presented at the Advances in Genome Biology and Technology General Meeting.
References:
1. Li, J.H., Mazur, C.A., Berisa, T., Pickrell, J.K. (2021). Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays. Genome Res. 31, 529-537.
2. Martin, A.R., Atkinson, E.G., Chapman, S.B., Stevenson, A., Stroud, R.E., Abebe, T., Akena, D., Alemayehu, M., Ashaba, F.K., Atwoli, L. (2021). Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. The American Journal of Human Genetics 108, 656-668.
3. Rubinacci, S., Ribeiro, D.M., Hofmeister, R.J., Delaneau, O. (2021). Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120-126.
4. Davies, R.W., Kucka, M., Su, D., Shi, S., Flanagan, M., Cunniff, C.M., Chan, Y.F., Myers, S. (2021). Rapid genotype imputation from sequence with reference panels. Nat. Genet. 53, 1104-1111.