Report Summary

Study Object

Genotyping enables researchers to explore genetic variants such as Single Nucleotide Polymorphisms(SNPs).
High-throughput genomic technologies such as Illumina Infinium SNP Genotyping Array enable a deeper understanding of disease etiology on a molecular level.
SNP genotyping data analysis tools can analyze results for millions of markers and probes and detect sample outliers, providing insight into the functional consequences of genetic variation.

Analysis Summary

24 Samples, 766221 SNPs were genotyped by GSA MG v2

SNP Clustering to call genotype

• using ready-made clustering file(*.egt)

Export genotype of 766221 SNPs to a text file per all samples.

Export *.ped & *.map file to execute PLINK.

Basic Information

	Description
Sample type	Genomic DNA
Organism	Homo sapiens
Platform	GSA MG v2
Scan protocol	Standard Illumina procedures using Illumina iScan scanner
Data processing	Normalized signal intensity and genotype were computed using Illumina’s GenomeStudio v.2 software.
Software	Illumina’s GenomeStudio v.2

I. Sample Information

I-1. Sample Information

Total 24 Samples

Index	Sample ID	p10 GC	p50 GC	Call Rate	Array Info.Sentrix ID	Array Info.Sentrix Position
1	Sample01	0.4015615	0.7867686	0.9851492	202878370113	R01C01
2	Sample02	0.4015615	0.787014	0.9856738	202878370113	R02C01
3	Sample03	0.4015615	0.7848412	0.9923821	202878370113	R03C01
4	Sample04	0.4015808	0.7871416	0.9861372	202878370113	R04C01
5	Sample05	0.4015615	0.7852078	0.9928311	202878370113	R05C01
6	Sample06	0.4015615	0.7852035	0.9929015	202878370113	R06C01
7	Sample07	0.4016134	0.78726	0.9859649	202878370113	R07C01
8	Sample08	0.4015615	0.7852834	0.9930373	202878370113	R08C01
9	Sample09	0.4015615	0.7852239	0.9928337	202878370113	R09C01
10	Sample10	0.4015615	0.7852577	0.9926366	202878370113	R10C01
11	Sample11	0.4015615	0.785257	0.9926601	202878370113	R11C01
12	Sample12	0.4015615	0.7851641	0.9923586	202878370113	R12C01
13	Sample13	0.4015615	0.785018	0.9918875	202878370113	R01C02
14	Sample14	0.401562	0.7870676	0.9857091	202878370113	R02C02
15	Sample15	0.4015912	0.7871504	0.9859649	202878370113	R03C02
16	Sample16	0.4015937	0.7871582	0.9857117	202878370113	R04C02
17	Sample17	0.4015656	0.787089	0.9857548	202878370113	R05C02
18	Sample18	0.4015615	0.7851323	0.9926653	202878370113	R06C02
19	Sample19	0.4015615	0.7851323	0.9926901	202878370113	R07C02
20	Sample20	0.4015615	0.7851323	0.99257	202878370113	R08C02
21	Sample21	0.4015615	0.7851323	0.9925609	202878370113	R09C02
22	Sample22	0.4015615	0.7851323	0.9924995	202878370113	R10C02
23	Sample23	0.4015853	0.7871226	0.9857678	202878370113	R11C02
24	Sample24	0.4015615	0.7851323	0.9920284	202878370113	R12C02

II. Platform Information

II-1. Illumina microarray solutions

Screening tools for analyzing genetic variation on any scale

High-throughput arrays for identifying nucleotide and structural changes in the human genome

https://www.illumina.com/techniques/microarrays.html

https://www.illumina.com/techniques/microarrays/human-genotyping.html

II-2. Experiment Methods

II-3. GSA MG v2 information

Link of annotation files & datasheet

	Link
1	Annotation File(GRCh37)
2	Data Sheet

III. Data Analysis

III-1. SNP genotyping

1. Clustering

• Make genotype calls across all samples using a standard Infinium Bead Chip cluster file.
• The standard cluster file (*egt file) supplied by Illumina for each Infinium BeadChip type is generated using a diverse set of more than 200 HapMap1DNA samples in an Illumina laboratory

2. Callrate check

• Quality checking by plotting p10 GC and sample call rate.
• If a sample passes the intact DNA sample QC criteria but when the callrate is significantly lower than other samples, then the sample can be re-experiment is some cases.

3. Genotype matrix export

• Make a text file that contains the genotype of entire samples and probes.

4. Make input files for third party tools

• Make *.ped & *.map files to execute PLINK.

IV. Result

IV-1. SNP genotyping

1. Raw data

• The resulting raw Intensity Data files (*.idat) produced by scanner.
  Naming rule: Sentrix ID_Sentrix Position_[Red|Grn].idat
• Please refer to RawData/idat folder.

2. Sample Table & QC

• Sample Table : Sample.Table.txt
• Quality check by plotting p10 GC & sample call rate

• Call Rate : Percentage of SNPs (expressed as a decimal) whose GenCall score is greater than the specified threshold.
• p10 GC : 10th percentile GenCall score over all SNPs for this sample. If displayed as 0.000, this column needs to be manually recalculated.
• GenCall Scrore : GenCall Score is a quality metric that indicates the reliability of each genotype call.
• 50% GenCall score, and 10% GenCall score are useful metrics for evaluating the quality and performance of DNA samples in an experiment.

3. Genotype matrix

• Genotype matrix text file : gtReport.txt

4. PLINK input files

• Please refer to SNP genotyping/plink input folder. (*.ped & *.map file)