Submission Details

Submission IDS00010
Submission Date2019-11-15 00:00:00
Submission Statusreviewing
SubmitterDavide Bagnara
Submitter Addressdavide.bagnara@edu.unige.it
SpeciesHuman
EthnicityUN

Inferred Sequences

The inferred novel alleles from each genotype that are submitted for review. This table lists all inferences put forward by the submitter. Where IARC has affirmed a sequence based on an inference, the corresponding sequence record will be listed in the Published column. Inferences for which no published sequence is shown have not been affirmed.

SequenceSubjectGenotypePublished
 IGHV1-69*14_S5279B12B12A00045
 IGHV2-70*01_S6619B12B12A00044
 IGHV4-61*01_S7407B12B12A00046
 IGHV1-69*01_S7220B16B16A00050
 IGHV4-4*08_S8301B16B16A00047
 IGHV4-59*01_S8652B16B16A00048
 IGHV4-61*01_S5549B16B16A00049
 IGHV2-70*04_S4496B16B16

Genotypes

Each genotype that has been inferred, along with the descriptive name of the inference tool and settings that were used.

Genotype NameSubject IDLocusSequence TypeGenotype FilenameTool/Setting Name
 B12B12IGHVSRR5408027_B12_ogrdb_report.csvIgDiscover
 B16B16IGHVSRR5408024_B16_ogrdb_report.csvIgDiscover

Acknowledgements

Individuals who should be acknowledged as contributing to the inferences listed in this submission.

NameInstitutionORCID ID
Martin CorcoranDepartment of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institute, Stockholm Sweden.

Repertoire Details

Details of the repertoire from which the inferences are based. This corresponds, for example, to an NIH Project or an ENA study.

RepositoryNCBI SRA
Accession NumberPRJNA381394
Project/Study TitleIg-seq_method
Dataset URLhttps://www.ncbi.nlm.nih.gov/bioproject/PRJNA381394
MiAIRR Compliant?No
MiAIRR URL
Sequencing PlatformMiseq
Read LengthR1=325 R2=285
Primers Overlapping?Yes

Repertoire Publications

Publications associated with this study.

PubMed IDTitleAuthors
28959265Novel Method for High-Throughput Full-Length IGHV-D-J Sequencing of the Immune Repertoire from Bulk B-Cells with Single-Cell Resolution.Vergani S, Korsunsky I, Mazzarello AN, Ferrer G, Chiorazzi N, Bagnara D

Sequences of the PCR primers used in the study.

RV CH region

reverse primers on the CH region (IgM, IgG, IgA) used for PCR amplification

Primer NamePrimer Sequence
HCA-n2mGGGAAGACCTTGGGGCTGGT
HCM-n2mAAAGGGTTGGGGCGGATGC
HCG-n2mGGAAGACCGATGGGCCCTT

FW Leader Primers

Primer NamePrimer Sequence
L3_VH1*GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCAACTACAGGTGCCCACTCC
L3_VH1-46GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNTAGCTCCAGGTGCTCACTCC
L3_VH1-69GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNNCAGCYACAGGTGTCCASTCC
L3_VH1-2GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCMACAGGWGCCCACTCC
L3_VH1-45GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNAGCCACAGATGCCTACTCC
L3_VH1-24GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNCTACAGGCACCCACGCC
L3_VH2GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNCCKTCCTGGGTCTTRTCC
L3_VH2-70*09GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCCTTCATGGGTCTTGTCT
L3_VH3*GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNTTWAAAGGTGTCCAGTGTGARG
L3_VH3-30/33/11GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNWTAARAGGTGTCCAGTGTCAGG
L3_VH4GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCCAGATGGGTCCTGYCC
L3_VH5-51GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNTTCTCCAAGGAGTCTGTKCC
L3_VH6-1GCGTCAGATGTGTATAAGAGACAGNNNNNNNNNNNNNNNCCATGGGGTGTCCTGTCA

Inference Tools and Settings

Details of the inference tools and settings used to infer novel alleles. Each combination of tool and setting is listed here, and provided with a descriptive name.

Tool/Settings NameTool NameTool Version
 IgDiscoverIgDiscover0.8.0+188.g8b9dbd8

Notes

No notes provided

Attachment File Name
 SRR5408027_B12_ogrdb_plots.pdf
 SRR5408024_B16_ogrdb_plots.pdf