NBDC Research ID: hum0335.v1
SUMMARY
Aims: Diagnosis of lymphoproliferative diseases, except for typical cases, is often pathologically difficult, and diagnosis has long been based on chromosome analysis, immunological traits, and genetic abnormalities. Recent advances in the comprehensive analysis of genetic abnormalities and immunological studies have led to a number of reports of new abnormalities and features that can lead to diagnosis, but diagnosis in clinical practice has not kept pace with these changes. In this study, we compared the clinical picture, including prognosis, of the current pathological diagnosis with that of a new diagnosis based on comprehensive analysis of genetic mutations and immunological traits that have not yet been incorporated into conventional clinical practice.
Methods: We created primers covering the coding regions of ARID1A, NOTCH2, CXCR4, MYD88, PRDM1, CD274, PDCD1LG2, RAG2, KMT2D, MYBBP1A, TP53, and CD79B and performed targeted sequencing using the NextSeq 500 next-generation sequencer. After annotation based on GRCh37/hg19, mutations that met the following criteria were filtered out: Read Depth < 500, Alt Variant Freq < 5% (< 1% on MYD88 L265P), global frequency > 1% or East Asian pop frequency > 1% based on 1000 Genomes Project, synonymous mutations, inflame mutations, and missense mutations scored “tolerated” by SIFT or “benign” by PolyPhen.
Participants/Materials: DNAs extracted from specimens from 10 cases of Waldenström macroglobulinemia and 10 cases of non IgM-type lymphoplasmacytic lymphoma (LPL)
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| DRA014819 | NGS (Target Capture) | Unrestricted-access | 2022/09/14 |
*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more
| Participants/Materials |
Waldenström macroglobulinemia (ICD10: C880): 10 cases 5 bone marrow mononuclear cells 1 peripheral blood mononuclear cell 2 bone marrow formalin-fixed paraffin-embedded (FFPE) specimens 2 lymph node FFPE specimens non IgM-type LPL (ICD10: C830): 10 cases 3 bone marrow mononuclear cells 3 peripheral blood mononuclear cells 4 bone marrow FFPE specimens |
| Targets | Target Capture |
| Target Loci for Capture Methods | ARID1A, NOTCH2, CXCR4, MYD88, PRDM1, CD274, PDCD1LG2, RAG2, KMT2D, MYBBP1A, TP53, CD79B |
| Platform | Illumina [NextSeq 500] |
| Library Source | DNAs extracted from bone marrow mononuclear cells, peripheral blood mononuclear cells, bone marrow FFPE specimens or lymph node FFPE specimens |
| Cell Lines | - |
| Library Construction (kit name) | AmpliSeq Custom DNA Panel for Illumina |
| Fragmentation Methods | - |
| Spot Type | Single-end |
| Read Length (without Barcodes, Adaptors, Primers, and Linkers) | 151 bp |
| DDBJ Sequence Read Archive ID | DRA014819 |
| Total Data Volume | 9.9 GB (bam [ref：GRCh37/hg19]) |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Akihiko Yokohama
Affiliation: Division of Blood Transfusion Service, Gunma University
Project / Group Name: "Waldenström macroglobulinemia and non-IgM-type lymphoplasmacytic lymphoma are genetically similar"
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| KAKENHI Grant-in-Aid for Scientific Research (C) | Amino acid transporter in malignant lymphoma; its analysis and clinical application | 16K10342 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | |||
| 2 |
