NBDC Research ID: hum0130.v1

 

SUMMARY

Aims: To compare genetic features of plasma cells from polyneuropathy, organomegaly, endocrinopathy, M-Protein, and skin changes (POEMS) syndrome, multiple myeloma (MM), and monoclonal gammopathy of undetermined significance (MGUS).

Methods: Genomic analysis of POEMS syndrome, and gene expression analysis of 3 dieases.

Participants/Materials: Plasma cells from POEMS syndrome, MM, and MGUS

 

Data Set IDType of DataCriteriaRelease Date
JGAS00000000150 NGS (Exome, Target Capture, RNA-seq) Controlled Access (Type I) 2019/01/18

*Release Note

* Data users need to apply the Form 2 (Application Form for Using NBDC Human Data) to reach the Controlled Access Data. Learn more

 

MOLECULAR DATA

Exome

Participants/Materials POEMS syndrome (ICD10: C90.2): 15 cases
Targets Exome
Target Loci for Capture Methods Coding exons
Platform Illumina [HiSeq 2500]
Library Source DNA purified from Plasma cells or buccal cell of POEMS syndrome, MM, MGUS
Cell Lines -
Library Construction (kit name) SureSelect Human ALL Exon V5
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end or Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 121 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000226
Total Data Volume 171 GB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

Target Capture

Participants/Materials POEMS syndrome (ICD10: C90.2): 20 cases
Targets Target Capture
Target Loci for Capture Methods Coding exons
Platform Illumina [MiSeq]
Library Source DNA purified from Plasma cells or buccal cell of POEMS syndrome, MM, MGUS
Cell Lines -
Library Construction (kit name) custom designed SureSelect XT2 Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Paired-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 273 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000226
Total Data Volume 171 GB (bam [ref: hg19])
Comments (Policies) NBDC policy

 

RNA-seq

Participants/Materials

POEMS syndrome (ICD10: C90.2): 5 cases

MM (ICD10: C90.0): 4 cases

MGUS (ICD10: D47.2): 5 cases

Targets RNA-seq
Target Loci for Capture Methods
Platform Illumina [HiSeq 1500]
Library Source RNA purified from Plasma cells or buccal cell of POEMS syndrome, MM, MGUS
Cell Lines -
Library Construction (kit name) SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing, NEBNext Ultra DNALibrary Prep Kit
Fragmentation Methods Ultrasonic fragmentation
Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 60 bp
Japanese Genotype-phenotype Archive Data set ID JGAD00000000226
Total Data Volume 171 GB (fastq)
Comments (Policies) NBDC policy

 

DATA PROVIDER

Principal Investigator: Emiko Sakaida

Affiliation: Chiba University Graduate school of Medicine, Clinical Cell Bilogy and Medicine

Project / Group Name:

Funds / Grants (Research Project Number):

NameTitleProject Number
KAKENHI Grant-in-Aid for Scientific Research (C) Genetic and transcriptional landscape of plasma cells in POEMS syndrome 26461397
KAKENHI Grant-in-Aid for Scientific Research (C) Clonal immunoglobulin lamda light-chain gene rearrangements detected by NGS in POEMS syndrome 15K09494

 

PUBLICATIONS

TitleDOIData Set ID
1 Genetic and transcriptional landscape of plasma cells in POEMS syndrome. doi: 10.1038/s41375-018-0348-x JGAD00000000226
2

 

USRES (Controlled-Access Data)

Principal Investigator: Affiliation: Data in Use (Data Set ID)Period of Data Use