データセット ID

NHA000190

Name: NHA000190: 腸内微生物叢のGWAS、血中代謝物のGWAS、KEGG Gene OrthologおよびKEGG PathwayのGWAS
Published: 2023-10-02

データの種類: 腸内微生物叢のGWAS
血中代謝物のGWAS
KEGG Gene OrthologおよびKEGG PathwayのGWAS
アクセス制限: 非制限公開
総データ量: 320 GB
ファイル形式: TSV
DOCX
研究: hum0197
公開日: 2023-10-02
更新日: 2023-10-02
Secondary ID: hum0197.v18.gwas.v1

このデータセットに紐づく非制限公開ファイル

URL の一覧のダウンロード

表示件数

20 50 100

401–450 / 732 件

ファイル名	ラベル	サイズ
microbiome_L7_species_Bifidobacterium_breve_QCed_sumstats.tsv.gz	Bifidobacterium_breve	525 MB
microbiome_L7_species_Bifidobacterium_catenulatum_QCed_sumstats.tsv.gz	Bifidobacterium_catenulatum	526 MB
microbiome_L7_species_Bifidobacterium_dentium_QCed_sumstats.tsv.gz	Bifidobacterium_dentium	525 MB
microbiome_L7_species_Bifidobacterium_gallinarum_QCed_sumstats.tsv.gz	Bifidobacterium_gallinarum	527 MB
microbiome_L7_species_Bifidobacterium_kashiwanohense_QCed_sumstats.tsv.gz	Bifidobacterium_kashiwanohense	526 MB
microbiome_L7_species_Bifidobacterium_longum_QCed_sumstats.tsv.gz	Bifidobacterium_longum	525 MB
microbiome_L7_species_Bifidobacterium_merycicum_QCed_sumstats.tsv.gz	Bifidobacterium_merycicum	526 MB
microbiome_L7_species_Bifidobacterium_moukalabense_QCed_sumstats.tsv.gz	Bifidobacterium_moukalabense	526 MB
microbiome_L7_species_Bifidobacterium_pseudocatenulatum_QCed_sumstats.tsv.gz	Bifidobacterium_pseudocatenulatum	527 MB
microbiome_L7_species_Bifidobacterium_pseudolongum_QCed_sumstats.tsv.gz	Bifidobacterium_pseudolongum	526 MB
microbiome_L7_species_Bifidobacterium_pullorum_QCed_sumstats.tsv.gz	Bifidobacterium_pullorum	525 MB
microbiome_L7_species_Bifidobacterium_reuteri_QCed_sumstats.tsv.gz	Bifidobacterium_reuteri	525 MB
microbiome_L7_species_Bifidobacterium_ruminantium_QCed_sumstats.tsv.gz	Bifidobacterium_ruminantium	527 MB
microbiome_L7_species_Bifidobacterium_saeculare_QCed_sumstats.tsv.gz	Bifidobacterium_saeculare	526 MB
microbiome_L7_species_Bifidobacterium_saguini_QCed_sumstats.tsv.gz	Bifidobacterium_saguini	525 MB
microbiome_L7_species_Bifidobacterium_scardovii_QCed_sumstats.tsv.gz	Bifidobacterium_scardovii	526 MB
microbiome_L7_species_Bifidobacterium_sp_QCed_sumstats.tsv.gz	Bifidobacterium_sp	524 MB
microbiome_L7_species_Bifidobacterium_stercoris_QCed_sumstats.tsv.gz	Bifidobacterium_stercoris	526 MB
microbiome_L7_species_Bifidobacterium_thermacidophilum_QCed_sumstats.tsv.gz	Bifidobacterium_thermacidophilum	527 MB
microbiome_L7_species_Bilophila_sp_QCed_sumstats.tsv.gz	Bilophila_sp	521 MB
microbiome_L7_species_Bilophila_wadsworthia_QCed_sumstats.tsv.gz	Bilophila_wadsworthia	525 MB
microbiome_L7_species_Blautia_hansenii_QCed_sumstats.tsv.gz	Blautia_hansenii	523 MB
microbiome_L7_species_Blautia_hydrogenotrophica_QCed_sumstats.tsv.gz	Blautia_hydrogenotrophica	526 MB
microbiome_L7_species_Blautia_luti_QCed_sumstats.tsv.gz	Blautia_luti	521 MB
microbiome_L7_species_Blautia_obeum_QCed_sumstats.tsv.gz	Blautia_obeum	521 MB
microbiome_L7_species_Blautia_producta_QCed_sumstats.tsv.gz	Blautia_producta	523 MB
microbiome_L7_species_Blautia_schinkii_QCed_sumstats.tsv.gz	Blautia_schinkii	523 MB
microbiome_L7_species_Blautia_sp_QCed_sumstats.tsv.gz	Blautia_sp	521 MB
microbiome_L7_species_Blautia_wexlerae_QCed_sumstats.tsv.gz	Blautia_wexlerae	522 MB
microbiome_L7_species_Burkholderiales_bacterium_QCed_sumstats.tsv.gz	Burkholderiales_bacterium	526 MB
microbiome_L7_species_Butyricicoccus_pullicaecorum_QCed_sumstats.tsv.gz	Butyricicoccus_pullicaecorum	526 MB
microbiome_L7_species_Butyricicoccus_sp_QCed_sumstats.tsv.gz	Butyricicoccus_sp	523 MB
microbiome_L7_species_Butyricimonas_virosa_QCed_sumstats.tsv.gz	Butyricimonas_virosa	525 MB
microbiome_L7_species_Butyrivibrio_crossotus_QCed_sumstats.tsv.gz	Butyrivibrio_crossotus	525 MB
microbiome_L7_species_Butyrivibrio_sp_QCed_sumstats.tsv.gz	Butyrivibrio_sp	522 MB
microbiome_L7_species_Caecibacter_massiliensis_QCed_sumstats.tsv.gz	Caecibacter_massiliensis	525 MB
microbiome_L7_species_Catenibacterium_mitsuokai_QCed_sumstats.tsv.gz	Catenibacterium_mitsuokai	526 MB
microbiome_L7_species_Catenibacterium_sp_QCed_sumstats.tsv.gz	Catenibacterium_sp	524 MB
microbiome_L7_species_Christensenella_timonensis_QCed_sumstats.tsv.gz	Christensenella_timonensis	526 MB
microbiome_L7_species_Citrobacter_freundii_QCed_sumstats.tsv.gz	Citrobacter_freundii	525 MB
microbiome_L7_species_Citrobacter_sp_QCed_sumstats.tsv.gz	Citrobacter_sp	522 MB
microbiome_L7_species_Clostridiaceae_bacterium_QCed_sumstats.tsv.gz	Clostridiaceae_bacterium	525 MB
microbiome_L7_species_Clostridiales_bacterium_QCed_sumstats.tsv.gz	Clostridiales_bacterium	525 MB
microbiome_L7_species_Clostridioides_difficile_QCed_sumstats.tsv.gz	Clostridioides_difficile	525 MB
microbiome_L7_species_Clostridium_asparagiforme_QCed_sumstats.tsv.gz	Clostridium_asparagiforme	526 MB
microbiome_L7_species_Clostridium_bolteae_QCed_sumstats.tsv.gz	Clostridium_bolteae	524 MB
microbiome_L7_species_Clostridium_butyricum_QCed_sumstats.tsv.gz	Clostridium_butyricum	525 MB
microbiome_L7_species_Clostridium_celatum_QCed_sumstats.tsv.gz	Clostridium_celatum	524 MB
microbiome_L7_species_Clostridium_celerecrescens_QCed_sumstats.tsv.gz	Clostridium_celerecrescens	526 MB
microbiome_L7_species_Clostridium_cf_QCed_sumstats.tsv.gz	Clostridium_cf	522 MB

401–450 / 732 件

解析手法

genome wide SNPs

材料と対象者: 日本人集団：524名（423種の微生物）
日本人集団：362名（306種の代謝物）
日本人集団：524名（KEGG Gene OrthologおよびKEGG Pathway）; 対象者数
524 (人数)
対象集団
日本人
試料説明: 末梢血から抽出したDNA; 組織
末梢血
腫瘍 / 非腫瘍
非腫瘍
実験方法: Genotyping by array
WGS
試薬キット: Infinium Asian Screening Array Kit
KAPA Hyper Prep Kit
TruSeq DNA PCR-Free Library Prep Kit
プラットフォーム: Illumina HiSeq 2500
Illumina HiSeq 3000
Illumina HiSeq X
Illumina Infinium Asian Screening Array
Illumina NovaSeq 6000
参照ゲノム: GRCh37
QC・フィルタリング: ・SNP array data：
サンプル QC：We excluded individuals with low genotyping call rates (call rate < 98%). We included individuals of the estimated Asian ancestry using PCA.
バリアント QC：We excluded variants with (1) genotyping call rate < 99%, (2) minor allele count < 5, (3) P-value for Hardy-Weinberg equilibrium < 1.0 × 10^−10, and (4) > 5% allele frequency difference compared with the imputation reference panel or the allele frequency panel of Tohoku Medical Megabank Project.
インピュテーション後のQC：We excluded imputed variants with Rsq < 0.7 and minor allele frequency < 1%.
・WGS：
We excluded variants with genotype call rate <90%, ExcessHet > 60, Hardy-Weinberg P<1.0×10−10
After imputation with Beagle v5.1, we excluded imputed variants with minor allele frequency < 1%.
インピュテーション: ハプロタイプフェージング: shapeit4
インピュテーション: minimac4
解析方法: ・SNP array:
遺伝子型決定: GenomeStudio
・WGS:
WA-MEM v0.7.13、GATK v3.8-0
PLINK2
バリアント数: 腸内微生物叢/KEGG (SNP array): 7,213,470 variants
血中代謝物 (WGS): 6,840,258 variants
加工データの種類: GWAS 要約統計量
表現型データの有無: あり
利用ポリシー: NBDC データ共有ポリシー (JGAP000001)