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illumina的Omni系列芯片进化史

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发表于 2017-2-14 11:28:32 | 显示全部楼层 |阅读模式
希望这个链接不要过时:https://www.illumina.com/Documen ... et_gwas_roadmap.pdf
也就是说,希望illumina公司不要倒闭!
Genome-wide association studies(GWAS) have identified hundreds ofcommon genetic variants associatedwith human diseases and providedvaluable insights into the geneticarchitecture behind many diseases.Building on this success, the 1,000Genomes Project (1KGP) is expectedto dramatically expand the catalog ofhuman genetic variants for the nextgeneration of GWAS, as the project willseek to identify nearly all variants thatexist at any appreciable frequency


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 楼主| 发表于 2017-2-15 15:16:29 | 显示全部楼层
芯片设计到的marker个数如下:
Illumina Infinium HumanExome BeadChip 1.0Affymetrix Genome Wide Human SNP Array 6.0Illumina HumanOmni 1Illumina Human Omni 2.5Illumina Human Omni 5Axiom Exome319
Total Number of Markers242901934969113451423798554301332319302
     Indel137045443453735138
     SNP242764934969113406023798124296795284164
     Exonic22457187185979162711129338269272
     Intronic5740343502365281855282158244512054
     Intergenic85615336245369711292448224045419229
     Others40294912517247116941434909518747



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 楼主| 发表于 2017-2-15 15:17:43 | 显示全部楼层
illumina的外显子芯片跟真正的外显子测序比较起来:

首先是成本
At a cost of less than $50 per chip, exome chips have become cost-effective alternatives to exome sequencing for large GWASs. Furthermore, exome chip data require less hard drive space for storage and processing than exome sequencing data.
然后是数据量:
For an exome chip genotyping project of 39,000 samples, ∼3.6 TB of storage is required to store and process the data. If the same size study were done by exome sequencing, ∼400 TB storage space could be required.
最后是功效
However, exome sequencing enables researchers to identify novel SNPs across the whole exome region plus some intron and intergenic regions
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 楼主| 发表于 2017-2-15 15:18:24 | 显示全部楼层
数据分析方法如下:

GenomeStudio section 这个是illumina自己开发的软件

Loading the data into GenomeStudio
Performing automatic clustering
QC on SNPs located in a haploid genome
QC based on GenTrain score
QC based on cluster separation
QC based on Mendelian error and replication error
QC based on other criteria
Calling rare SNPs
Final fltering
Exporting from GenomeStudio

Post-GenomeStudio section还需要用其它软件

Converting all SNPs to the forward strand
Checking for gender mismatch
Checking for race mismatch
Checking for relatedness
Checking for Hardy-Weinberg equilibrium (HWE) outliers
Checking for heterozygosity outliers
Checking consistency between exome chip genotype and 1000 Genomes Project17 or HapMap18 genotype
Checking for minor allele frequency (MAF) consistency between exome chip and 1000 Genomes Project genotypes
Checking for batch effects
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 楼主| 发表于 2017-2-15 15:20:39 | 显示全部楼层
这篇文章可以看一看:Illumina human exome genotyping array clustering and quality control
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4441213
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