三種方法如何獲取snp信息
引用: http://www.bio-info-trainee.com/2100.html#more-2100
有研究表明STAT4上的rs7574865和HLA-DQ的 rs9275319是人群中乙型肝炎病毒（HBV）相關(guān)肝細(xì)胞癌（HCC）遺傳易感基因
意思是，某兩個位點變異導(dǎo)致乙型肝炎病毒和相關(guān)肝細(xì)胞癌發(fā)生的關(guān)鍵原因。rsID分別代表兩個變異位點 （發(fā)現(xiàn)變異位點后通過vep/snpEFF對變異位點進(jìn)行的注釋）。所以根據(jù)rsID能夠找到這個位點在基因組的位置。可以用dnSNP來查看rsID的基因坐標(biāo)。
方法一：
下載All_20160601.vcf.gz 這個文件（很大數(shù)據(jù)）:
mkdir -p ~/annotation/variation/human/dbSNP
cd ~/annotation/variation/human/dbSNP
## https://www.ncbi.nlm.nih.gov/projects/SNP/
## ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh38p2/
## ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/
nohup wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/All_20160601.vcf.gz &
wget ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b147_GRCh37p13/VCF/All_20160601.vcf.gz.tbi
運行的時候有報錯：No such directory ‘snp/organisms/human_9606_b147_GRCh37p13/VCF’.
方法二：
也可以登錄網(wǎng)頁版本數(shù)據(jù)庫，直接修改 url（小量搜索）：
https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=7574865
https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs9275319
方法三：
SNPedia，直接修改url （優(yōu)點，搜集了非常多的其它數(shù)據(jù)庫的鏈接）
https://www.snpedia.com/index.php/Rs7574865
https://www.snpedia.com/index.php/Rs9275319
拓展：如何進(jìn)行GWAS分析
方法一：
plink進(jìn)行分析
這里是plink的官網(wǎng)：https://www.cog-genomics.org/plink2/
plink做SNP篩選和GWAS
plink進(jìn)行GWAS分析
方法二：
R包分析 （繪制曼哈頓圖）
Postgwas: Advanced GWAS Interpretation in R
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071775
如何call SNP and indels
參考： http://blog.sina.com.cn/s/blog_83f77c940102w2eb.html
如何SNP過濾
引用： http://blog.sina.com.cn/s/blog_83f77c940102w2eg.html
- 缺失比例 （Missing rates）
GENO>0.05
Shortly we will apply more stringent criteria, such that GENO > 0.05. In this case, 0.05*89 = 4.45 samples, meaning that if a SNP is missing in 4.45 more more samples, that SNP will be removed from the dataset.
89是全部sample數(shù)，89xGENO得到的閥值是4.45，所以某個call的SNP在4樣品（或以下）里沒有出現(xiàn)，保留；在5個樣本以上沒出現(xiàn)則刪掉。
- 最小等位基因頻率 （Minor Allele frequencies）
提示： MAF< 0.03 如果SNP較多可以設(shè)置為MAF<0.05
MAF is the Minor Allele Frequency. It can be used to exclude SNPs which are not informative because they show little variation in the sample set being analyzed. For instance, if a SNP shows variation in only 1 of the 89 individuals, it is not useful statistically and should be removed.
意思是，如果某一個SNP只出現(xiàn)在很少數(shù)樣品（< MAF x Total Number of samples)的時候，就需要移除
- Removing SNPs out of Hardy-Weinberg equilibrium(p-value > 10^6 - 10^4 ) 哈迪溫伯格平衡
Population genetic theory suggests that under ‘normal’ conditions, there is a predictable relationship between allele frequencies and genotype frequencies. In cases where the genotype distribution is different from what one would expect based on the allele frequencies, one potential explanation for this is genotyping error. Natural selection is another explanation. For this reason, we typically check for deviation from Hardy-Weinberg equilibrium in the controls for a case- control study. For a quantitative trait, PLINK just uses everyone. The following command generates p-values for deviation from HWE for each SNP. Low p-values indicate that a SNP is out of HWE.
- 由vcf文件進(jìn)行SNP過濾
運用vcftools轉(zhuǎn)換為plink的輸入形式，輸出 bed文件 （或者map文件），然后作為輸入進(jìn)行過濾
vcftools --vcf my.vcf --plink --out plink
plink --noweb --file plink --geno 0.05 --maf 0.05 --hwe 0.0001 --make-bed --out QC
如果還不知道什么是GWAS？什么是SNP？這里是定義：
引用： http://www.biotrainee.com:8080/thread-1487-1-1.html
Genome-wide association studies (GWAS) 是指在人類全基因組範(fàn)圍內(nèi)利用存在的序列變異，即單核苷酸多型性(SNP)，並從中篩選出與疾病相關(guān)的SNPs。
- 哪些疾病與SNP有關(guān)呢？
近些年，全基因組關(guān)聯(lián)分析方法（Genome-Wide Association Study，簡稱GWAS）利用大群體和高密度SNP（Single Nucleotide Polymorphism，單核苷酸多態(tài)）分子標(biāo)記已經(jīng)定位到了上千個與復(fù)雜疾病關(guān)聯(lián)的SNP位點，而且這些關(guān)聯(lián)信號在多次試驗中有很高的可重復(fù)性。比如人類常見疾病肥胖，糖尿病，精神分裂等。 - SNP的誤差因素？
由于隨機(jī)采樣帶來到抽樣誤差（這在現(xiàn)實中無法避免）以及SNP之間復(fù)雜的連鎖不平衡（linkage disequilibrium, 簡稱LD），GWAS定位到的SNP位點通常不是致病位點。
2016年發(fā)表在PLOS-one上的文章，介紹SNP與骨關(guān)節(jié)炎。
雖然不是很牛的雜志，但是文章質(zhì)量很好。
Functional Characterization of the Osteoarthritis Susceptibility Mapping to CHST11—A Bioinformatics and Molecular Study
根據(jù)標(biāo)題可以知道，是對Osteoarthritis疾病的研究，針對的目標(biāo)基因是CHST11，Carbohydrate sulfotransferase 11 is an enzyme that in humans is encoded by the CHST11 糖-磺基轉(zhuǎn)移酶 （不知道具體翻譯，請（生）化學(xué)大神指教）。基因位置 是 chr12: 104,455,295-104,762,014 (GRCh38)。CHST11的功能研究，英國劍橋的桑格研究所有做過該基因敲除的小鼠，Chst11^tm1a(KOMP)Wtsi 。這個基因主要與骨頭和軟骨的表型phenotyping有關(guān)系。小鼠的表型研究里發(fā)現(xiàn)異常：Homozygous viability at P14。
2012年柳葉刀里也有文章說這個基因突變會導(dǎo)致，骨關(guān)節(jié)炎，這個雜志就不用說有多厲害了。
Identification of new susceptibility loci for osteoarthritis (arcOGEN): a genome-wide association
接下來分別看一下這兩篇文章，和這個基因，以及這個基因的SNP，以及對其功能分析上的研究與闡述。
(一) 骨關(guān)節(jié)炎的背景：
什么是OA？
（1）Osteoarthritis (OA) is a common disease of older individuals that is characterized by the focal(病灶點) loss of articular cartilage. This loss usually occurs gradually over many years and typically results in chronic pain and severely impaired joint function by the sixth or seventh decade of life.
（2）Osteoarthritis is the most common form of arthritis worldwide and is a major cause of pain and disability in elderly people.
genetics上OA的特點？
（1）OA is polygenic and unlike many other common arthritic diseases, there are no OA risk- conferring loci of large singular impact
（2）It is a complex disease of the musculoskeletal system with both genetic and environmental risk factors. From the results of heritability studies in twins, sibling pairs, and families, genetic factors are estimated to account for about 50% of the risk of developing osteoarthritis in the hip or knee, although precise estimates vary according to sex, affected site, and severity of disease.
（二）研究方法：
（1）偏重功能分析
- Identification of SNPs in LD with rs835487
- Identification of Sequences Homologous to the Enhancer in Non-Human Mammals
- Cloning of pGL3-Promoter Luciferase Reporter Plasmids
- Transfection of Cell Lines
- Electrophoretic Mobility Shift Assays (EMSAs)
- Ethics Statement, Cartilage Collection and Nucleic Acid Extraction
- Gene Expression, Genotyping and AEI Analysis
- Chondrogenic Differentiation of MSCs
（2）偏重分析
- We undertook a large genome-wide association study (GWAS) in 7,410 unrelated and retrospectively and prospectively selected patients with severe osteoarthritis in the arcOGEN study, 80% of whom had undergone total joint replacement, and 11,009 unrelated controls from the UK. We replicated the most promising signals in an independent set of up to 7,473 cases and 42,938 controls, from studies in Iceland, Estonia, the Netherlands, and the UK. All patients and controls were of European descent.
(三）結(jié)論
（1）rs835487 (allele G; THR) located within intron two of CHST11 is associated with hip OA
