2020-10-05 genotype calling

Genotype-calling algorithms use normalized measures of DNA binding to allele specific probes to ascertain the genotype of an individual at a given SNP.

基因型调用算法使用DNA与等位基因特异性探针结合的标准化测量来确定给定SNP个体的基因型

low-frequency and rare variants (those with minor allele frequencies 0.5–5% and <0.5%, respectively; The 1000 Genomes Project Consortium, 2010)

Pathway- and network-based methodologies applied to GWAS aim to detect associations missed by standard single-marker approaches. The complex and non-random architecture of the genome makes it a challenge to derive an appropriate testing framework for such methodologies.

应用于GWAS的基于路径和网络的方法旨在检测标准单标记方法遗漏的关联。基因组结构的复杂性和非随机性使得为这种方法推导一个合适的测试框架成为一个挑战。

With high-throughput DNA sequencing costs dropping $1000 for human genomes, data storage, retrieval and analysis are the major bottlenecks in biological studies.

PubMed 23751181

Our results indicate that the mapping difficulty of the reads

that involve significant mismatches is the main limitation to

our matching mechanism and other split read methods. This

also highlights what others have found in comparing different

CNV discovery methods that each method has its own strength

and weaknesses and they usually complement each other (Teo

et al., 2012). Our method should be applied in combination

with other methods that utilize read depths and mapping distances information. When there are enough junction reads, our

method can be applied to identify the exact breakpoints of

the CNVs

PUBMED 23967014 discussion

A recurrent CNV region is often defined as a set of consecutive probes that are altered in a group of samples

24642062

1.This obstacle can be partially bypassed by implementing the mixed linear model, which uses the genetic relationship

between individuals estimated from single nucleotide polymorphism (SNP) markers

GWAS mixed linear model in lieu of fitting hundreds of thousands of markers together

24817879

Copy number variations (CNVs) are a form of a structural

genomic variation referring to duplications and deletions

of DNA segments larger than 1 kilobase in size. CNVs are

abundant in the human genome, and it is estimated that

they can occupy as much as 4% to 6%

Analysis of Variable，ANOVA（方差分析）