## Study Submission Type Short genetic variations Submitter Last Name Kawai Submitter Middle Name Submitter First Name Yosuke Submitter Affiliation National Center for Global Health and Medicine Study Title Construction of control data for the promotion of genomic medicine for cancers and rare diseases Study Description Whole genome sequencing is being promoted for better medical care of rare diseases and cancers. For these disease genome analyses, whole genome sequencing (WGS) analysis data of the healthy control group is necessary. We conducted WGS analysis of healthy individuals for cancers and rare diseases from biobank specimens held by six National Centers (NCs) Biobanks in Japan, taking regional variations into consideration, and construct a genome database of healthy individuals and disease control groups. Study Type Control Set PubMed ID 38060463 Publication DOI 10.1371/journal.pgen.1010625 BioProject Accession PRJDB18486 Study URL https://humandbs.dbcls.jp/en/hum0331-v1 Related Study Study ID Kawai2024b Submission Date 2024-01-23 Public Release Date 2024-07-22 Last Update Date ## SampleSet # SampleSet ID SampleSet Size SampleSet Type SampleSet Name SampleSet Description SampleSet Phenotype SampleSet Population SampleSet Sex 1 20994 Control NCGM NCGM ## Sample # BioSample Accession Sample Name Subject ID SampleSet ID Sample Resource Sample Cell Type Sample Attribute Sample Karyotype Subject Collection Subject Phenotype Subject Population Subject Karyotype Subject Sex Subject Age Subject Age Units Subject Maternal ID Subject Paternal ID SAMD00802407 JPN not applicable 1 sample size: 9290, description: NCBN sample that falls into the Japanese cluster in the PCA plot. They include all samples from JPN_Hondo and JPN_Ryukyu, as well as samples located in the middle of those clusters. Japanese SAMD00802408 JPN_Hondo not applicable 1 sample size: 9036, description: Samples belonging to the largest cluster comprising the JPN. Japanese SAMD00802409 JPN_Ryukyu not applicable 1 sample size: 186, description: Samples belonging to the smaller clusters that make up the JPN. Presumed to be individuals with ancestry in the Ryukyu Islands. Japanese SAMN07488236 ACB not applicable 1 sample size: 94, description: African Caribbean in Barbados (1000 Genomes) 1000 Genomes African-Caribbean SAMN07488235 ASW not applicable 1 sample size: 56, description: African Ancestry in Southwest US (1000 Genomes) 1000 Genomes African-American SW SAMN07488215 BEB not applicable 1 sample size: 85, description: Bengali in Bangladesh (1000 Genomes) 1000 Genomes Bengali SAMN07488225 CDX not applicable 1 sample size: 93, description: Chinese Dai in Xishuangbanna, China (1000 Genomes) 1000 Genomes Dai Chinese SAMN07488216 CEU not applicable 1 sample size: 98, description: Utah residents (CEPH) with Northern and Western European ancestry (1000 Genomes) 1000 Genomes CEPH SAMN07488224 CHB not applicable 1 sample size: 103, description: Han Chinese in Beijing, China (1000 Genomes) 1000 Genomes Han Chinese SAMN07488221 CHS not applicable 1 sample size: 104, description: Han Chinese South (1000 Genomes) 1000 Genomes Southern Han Chinese SAMN07488229 CLM not applicable 1 sample size: 92, description: Colombian in Medellin, Colombia (1000 Genomes) 1000 Genomes Colombian SAMN07488234 ESN not applicable 1 sample size: 98, description: Esan in Nigeria (1000 Genomes) 1000 Genomes Esan SAMN07488219 FIN not applicable 1 sample size: 99, description: Finnish in Finland (1000 Genomes) 1000 Genomes Finnish SAMN07488220 GBR not applicable 1 sample size: 91, description: British in England and Scotland (1000 Genomes) 1000 Genomes British SAMN07488214 GIH not applicable 1 sample size: 102, description: Gujarati Indian in Houston, TX (1000 Genomes) 1000 Genomes Gujarati SAMN07488233 GWD not applicable 1 sample size: 113, description: Gambian in Western Division, The Gambia (1000 Genomes) 1000 Genomes Gambian SAMN07488218 IBS not applicable 1 sample size: 107, description: Iberian populations in Spain (1000 Genomes) 1000 Genomes Spanish SAMN07488213 ITU not applicable 1 sample size: 102, description: Indian Telugu in the UK (1000 Genomes) 1000 Genomes Indian SAMN07488223 JPT not applicable 1 sample size: 104, description: Japanese in Tokyo, Japan (1000 Genomes) 1000 Genomes Japanese SAMN07488222 KHV not applicable 1 sample size: 99, description: Kinh in Ho Chi Minh City, Vietnam (1000 Genomes) 1000 Genomes Kinh Vietnamese SAMN07488232 LWK not applicable 1 sample size: 96, description: Luhya in Webuye, Kenya (1000 Genomes) 1000 Genomes Luhya SAMN07488231 MSL not applicable 1 sample size: 85, description: Mende in Sierra Leone (1000 Genomes) 1000 Genomes Mende SAMN07488228 MXL not applicable 1 sample size: 64, description: Mexican Ancestry in Los Angeles, California (1000 Genomes) 1000 Genomes Mexican-American SAMN07488227 PEL not applicable 1 sample size: 84, description: Peruvian in Lima, Peru (1000 Genomes) 1000 Genomes Peruvian SAMN07488212 PJL not applicable 1 sample size: 96, description: Punjabi in Lahore, Pakistan (1000 Genomes) 1000 Genomes Punjabi SAMN07488226 PUR not applicable 1 sample size: 104, description: Puerto Rican in Puerto Rico (1000 Genomes) 1000 Genomes Puerto Rican SAMN07488211 STU not applicable 1 sample size: 99, description: Sri Lankan Tamil in the UK (1000 Genomes) 1000 Genomes Sri Lankan SAMN07488217 TSI not applicable 1 sample size: 107, description: Toscani in Italia (1000 Genomes) 1000 Genomes Tuscan SAMN07488230 YRI not applicable 1 sample size: 107, description: Yoruba in Ibadan, Nigeria (1000 Genomes) 1000 Genomes Yoruba ## Experiment # Experiment ID Experiment Type Method Type Analysis Type Reference Type Reference Value Merged Experiment IDs Experiment Resolution Method Platform Method Description Analysis Description Detection Method Detection Description External Links 1 Discovery Sequencing Paired-end mapping Assembly GRCh38 Illumina NovaSeq 6000 DNA samples that meet the criteria for the study will be shipped from the biobank and subjected to WGS analysis at a contract analysis laboratory. WGS analysis will be performed on a Novaseq6000 sequencer using a PCR-free protocol to obtain a minimum output of 90 Gb. - Confirm library size is 400bp-750bp. - At least 75% of the bases are QV30 or better. - Total number of bases after removal of duplicate reads by FASTQC is more than 90 GBase. The read data in fastq format obtained from the analysis will be subjected to data analysis (mapping and variant calling) at the principal institute (National Center for Global Health and Medicine), and the data including variant information will be made into a database. - Samples with abnormal values for depth and mapping rate. - Samples where the depth of the sex chromosome is inconsistent with the clinical information. - Any of the samples determined to be within the second degree of kinship in the KING program. Variant call results were filtered for the following - Genotypes with GQ64 or with less than 25% minor alleles in heterozygous calls are set to no call - Set VQSR results to FILTER field in VCF - Set LowCR in FILTER field for variants with less than 95% call rate - Variants with a Hardy-Weinberg equilibrium test P-value less than 10-6 have HWE set in FILTER field HaplotypeCaller (GATK4.1.0) compatible algorithm (Parabricks 3.1.0 haplotypecaller) ## Dataset # Dataset ID SampleSet ID Experiment ID Number of Chromosomes Sampled Dataset Description Linkout URL submitted/VCF Filename 1 1 1 23544 chromosome 1 submitted/chr1.vcf 2 1 1 23544 chromosome 2 submitted/chr2.vcf 3 1 1 23544 chromosome 3 submitted/chr3.vcf 4 1 1 23544 chromosome 4 submitted/chr4.vcf 5 1 1 23544 chromosome 5 submitted/chr5.vcf 6 1 1 23544 chromosome 6 submitted/chr6.vcf 7 1 1 23544 chromosome 7 submitted/chr7.vcf 8 1 1 23544 chromosome 8 submitted/chr8.vcf 9 1 1 23544 chromosome 9 submitted/chr9.vcf 10 1 1 23544 chromosome 10 submitted/chr10.vcf 11 1 1 23544 chromosome 11 submitted/chr11.vcf 12 1 1 23544 chromosome 12 submitted/chr12.vcf 13 1 1 23544 chromosome 13 submitted/chr13.vcf 14 1 1 23544 chromosome 14 submitted/chr14.vcf 15 1 1 23544 chromosome 15 submitted/chr15.vcf 16 1 1 23544 chromosome 16 submitted/chr16.vcf 17 1 1 23544 chromosome 17 submitted/chr17.vcf 18 1 1 23544 chromosome 18 submitted/chr18.vcf 19 1 1 23544 chromosome 19 submitted/chr19.vcf 20 1 1 23544 chromosome 20 submitted/chr20.vcf 21 1 1 23544 chromosome 21 submitted/chr21.vcf 22 1 1 23544 chromosome 22 submitted/chr22.vcf 23 1 1 18782 chromosome X submitted/chrX.vcf