genome-wide association study in esophageal cancer using genechip mapping 10k array nan hu,1 chaoyu...
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Genome-Wide Association Study in Esophageal Cancer Using GeneChip Mapping 10K Array
Nan Hu,1 Chaoyu Wang,1 Ying Hu,2 Howard H. Yang,2 Carol Giffen,5 Ze-Zhong Tang,6 Xiao-Yu Han,6Alisa M. Goldstein,4 Michael R. Emmert-Buck,3 Kenneth H. Buetow,2 Philip R. Taylor,1and Maxwell P. Lee2
• AbstractAbstract• IntroductionIntroduction• Materials and MethodsMaterials and Methods• Results and DiscussionResults and Discussion
Abstract
• 找 Esophageal squamous cell carcinoma (ESCC) 病患的可能遺傳基因。
• 分別 correct 50 病患 與 50 正常人的 DNA. 分析每個 DNA 中 10,000 SNP 的序列。
• 比較病患與正常人的這 10,000 SNP --> 找到 37 個特別的 SNPs
• 37 個特別的 SNPs 與已知的 cancers 相關的基因有關。
•AbstractAbstract•IntroductionIntroduction•Materials and MethodsMaterials and Methods•Results and DiscussionResults and Discussion
Introduction
• ESCC is one of the most common malignancies in the Chinese (Shanxi Province)
• 目前已經知道 susceptibility biomarkers involved in ESCC 。但是 ...............
• Association studies with 10,000 SNP -> 遺傳基因
Esophageal squamous cell carcinoma (ESCC)
• 鳞状细胞癌：占食管癌的 90% 以上
• 发生于食管鳞状上皮 • 以食管中段为最多，
其次为下段。
食道鳞状细胞癌 (ESCC)
The foundation of genetics
Mendel's laws– 1. Law of unit characters
• Paired alleles control the inheritance of traitsHomozygous vs Heterozygous
AA Aa aa
SNP
DNA Sequence
GATATTCGTACGGA-TGATGTTCGTACTGAATGATATTCGTACGGA-TGATATTCGTACGGAATGATGTTCGTACTGAATGATGTTCGTACTGAAT
SN
P
SN
P
1 2
3
4
5 6
AG- 2/6GTA 3/6AGA 1/6
Phenotype
Black eyeBrown eyeBlack eyeBlue eyeBrown eyeBrown eye
AA
Aa
aa
Cancer (50) Normal (50)
50
0
0
0
0
50
Association studies
AA Aa aa
Odds Ratio (OR)
Disease
Disease Unaffected
Risk Factor+ p+D p+U
- p-D p-U
Association studies
Examples: Alzheimer’s • Alzheimer’s disease and ApoE
E4 present E4 absent
Patients 58 33
Controls 16 55
The E4 allele appears to be positively associated with Alzheimer’s disease:
Odds Ratio = (58/16)/(33/55) = 6
LOD : log odds ratio 有相關
Affymetrix (10,000)
Each spot may be AAAaaa
• AbstractAbstract• IntroductionIntroduction• Materials and MethodsMaterials and Methods• Results and DiscussionResults and Discussion
Patients and Controls
• 人體試驗委員會同意 (IRB) 。• 50 patients (males)
25 with a positive family history of ESCC25 without a family history of ESCC
• 50 Controls (males) Age-, sex-, and ancestral home for al
l controls was in Shanxi Province.
Biological Specimen Collection and Processing
• collect Patients and Control 血液檢體 (10 mL) 。
• 血液檢體 --> extract Genomic DNA 。
• Affymetrix 10K Chip analysis with 500 ng DNA 。
• 統計分析 (Association studies)
GeneChip Mapping 10K Array
major benefits 1. Requires only 250 ng of genomic DNA per sam
ple2. Easy-to-use (within 2 days)3. Get 10,000 SNPs genotyping
Affymetrix GA2500 Genechip System
GeneChip® Mapping Assay Overview(2)
Patients and Controls Information
• ‘‘Signal Detection Rate’’ is the percentage of SNPs that pass the discrimination filter.
• ‘‘Call Rate’’ is the percentage of SNPs called on the array.
榨菜
11560
Principal ComponentsAnalysis (PCA)
10k array
Patients controls
找出最符合的SNP ( n = 37)(n = 3000)
•確認資料的形態 •同時表現資料中的相同和差異 •容易歸納資料
• AbstractAbstract• IntroductionIntroduction• Materials and MethodsMaterials and Methods• Results and DiscussionResults and Discussion
找出最符合的 SNP ( n = 37)
RandomSNP ( n = 3000)
Figure 1. PCA analysis of cases and controls using multiloci genotypes. We used A allele as the recessive allele for genotype coding (AA, AB, BB) =(1, 0, 0). E, cases (red); N, controls (green). Details of the PCA can be found in Materials and Methods. A, X axis and Y axis, first and second principal components of PCA analysis using 37 SNPs from the 10K chip genotypes of 50 cases and 50 controls. B, X axis and Y axis, first and second principal components of PCA analysis using 3,369 SNPs (all SNPs with no missing genotype data) from the 10K chip genotypes of 50 cases and 50 controls.
The foundation of genetics
Mendel's laws (cont.)– 2. Law of dominance (cont.)Dominant, 顯性 (AA, Aa) vs Recessive, 隱性 (aa)
• 碗豆的特徵因素種子：平滑圓形 (顯性 )或皺紋種子內部顏色：黃色 (顯性 )或綠色未成熟豆夾的顏色：綠色 (顯性 )或黃色成熟豆夾的形態：膨脹 (顯性 )或壓縮花的顏色：紫色 (顯性 )或白色。花的位置：枝腋 (顯性 )或枝頂。莖的長度：短 (9-18 英吋 )或長 (6-7 英呎 )( 顯性 )
AA
Aa
aa
Cancer (50) Normal (50)
50
0
0
0
0
50
AA
Aa+aa
Cancer (50) Normal (50)
50
0
0
50
Association studies
Dominant, 顯性 (AA, Aa) vs Recessive, 隱性 (aa)
Continuous
AA Aa aa50% 25% 5%
Recessive
DominantAA+Aa aa50% 5%
AA Aa + aa50% 5%
Questions?