Analysis of SNPs in pooled DNA: A decision theoretic model

A permutation test for oligoset DNA pooling studies

Case-control association studies often suffer from population stratification bias. A previous triple combination strategy of stratum matching, genomic controlling, and multiple DNA pooling can correct the bias and save genotyping cost. However the method requires researchers to prepare a multitude of DNA pools-more than 30 case-control pooling sets in total (polyset). In this paper, the authors propose a permutation test for oligoset DNA pooling studies. Monte-Carlo simulations show that the proposed test has a type I error rate under control and a power comparable to that of individual genotyping. For a researcher on a tight budget, oligoset DNA pooling is a viable option.

A triple combination strategy corrects population stratification bias and saves genotyping cost

OBJECTIVE

The case-control association study has gained popularity for mapping disease-susceptibility gene(s) of complex human diseases. However, the study is prone to population stratification bias.

STUDY DESIGN AND SETTING

The authors proposed a triple combination strategy of stratum matching, genomic control, and multiple DNA pooling for population-based case-control association studies. Monte Carlo simulation showed that the type I error rates are well controlled using this strategy.

RESULTS

As for power, it increases under the following situations: (1) more accurate stratum matching, (2) more null markers for genomic control, (3) more DNA pooling sets, and (4) more accurate DNA pooling measurement.

CONCLUSION

The triple combination strategy corrects population stratification bias and saves genotyping cost.

Calmodulin-binding transcription activator 1 ( CAMTA1 ) alleles predispose human episodic memory performance

Little is known about the genes and proteins involved in the process of human memory. To identify genetic factors related to human episodic memory performance, we conducted an ultra-high-density genome-wide screen at > 500 000 single nucleotide polymorphisms (SNPs) in a sample of normal young adults stratified for performance on an episodic recall memory test. Analysis of this data identified SNPs within the calmodulin-binding transcription activator 1 (CAMTA1) gene that were significantly associated with memory performance. A follow up study, focused on the CAMTA1 locus in an independent cohort consisting of cognitively normal young adults, singled out SNP rs4908449 with a P-value of 0.0002 as the most significant associated SNP in the region. These validated genetic findings were further supported by the identification of CAMTA1 transcript enrichment in memory-related human brain regions and through a functional magnetic resonance imaging experiment on individuals matched for memory performance that identified CAMTA1 allele-specific upregulation of medial temporal lobe brain activity in those individuals harboring the 'at-risk' allele for poorer memory performance. The CAMTA1 locus encodes a purported transcription factor that interfaces with the calcium-calmodulin system of the cell to alter gene expression patterns. Our validated genomic and functional biological findings described herein suggest a role for CAMTA1 in human episodic memory.

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays

Robust estimation of allele frequencies in pools of DNA has the potential to reduce genotyping costs and/or increase the number of individuals contributing to a study where hundreds of thousands of genetic markers need to be genotyped in very large populations sample sets, such as genome wide association studies. In order to make accurate allele frequency estimations from pooled samples a correction for unequal allele representation must be applied. We have developed the polynomial based probe specific correction (PPC) which is a novel correction algorithm for accurate estimation of allele frequencies in data from high-density microarrays. This algorithm was validated through comparison of allele frequencies from a set of 10 individually genotyped DNA's and frequencies estimated from pools of these 10 DNAs using GeneChip 10K Mapping Xba 131 arrays. Our results demonstrate that when using the PPC to correct for allelic biases the accuracy of the allele frequency estimates increases dramatically.

A DNA Pooling Strategy for Family-Based Association Studies

Genome-wide association scans for disease susceptibility genes of complex diseases require genotyping on a massive scale. A DNA pooling strategy for family-based association studies is described, which is robust to population stratification biases and to errors in pooling. It can achieve a statistical efficiency of 0.95 with approximately 1 of 8 or fewer genotyping efforts, and an efficiency of 0.90 with approximately 1 of 16 or fewer efforts compared with individual genotyping. The pooling method described in this article provides a tradeoff between genotyping efforts and subject recruitment efforts.