Submission Details

Submission IDS00031
Submission Date2021-08-29 00:00:00
Submission Statusreviewing
SubmitterWilliam Lees
Submitter AddressBirkbeck College, University of London, Malet Street, London
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
 IGHV3-21*01_A184G_T190A_A191CS76P1_I80_S1A00065
 IGHV1-69*04_C184TS47P1_I50_S1A00066
 IGHV3-30*19_T189CS46P1_I49_S1A00067
 IGHV3-33*01_G75CS43P1_I46_S1A00068
 IGHV3-9*01_T307CS82P1_I86_S1A00069
 IGHV4-39*01_C66GS86P1_I90_S1A00070
 IGHV4-39*07_C288AS29P1_I29_S1A00071
 IGHV4-4*02_A106GS39P1_I42_S1A00072
 IGHV4-61*02_A234GS82P1_I86_S1A00073

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
 P1_I80_S1S76IGHVP1_I80_S1_ogrdbstats.csvTigger
 P1_I50_S1S47IGHVP1_I50_S1_ogrdbstats.csvTigger
 P1_I49_S1S46IGHVP1_I49_S1_ogrdbstats.csvTigger
 P1_I46_S1S43IGHVP1_I46_S1_ogrdbstats.csvTigger
 P1_I86_S1S82IGHVP1_I86_S1_ogrdbstats.csvTigger
 P1_I90_S1S86IGHVP1_I90_S1_ogrdbstats.csvTigger
 P1_I29_S1S29IGHVP1_I29_S1_ogrdbstats.csvTigger
 P1_I42_S1S39IGHVP1_I42_S1_ogrdbstats.csvTigger

Acknowledgements

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

No Items

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 NumberPRJEB26509
Project/Study TitleIllumina MiSeq paired end sequencing
Dataset URLhttps://www.ncbi.nlm.nih.gov/sra/?term=PRJEB26509
MiAIRR Compliant?No
MiAIRR URL
Sequencing PlatformIllumina
Read Length300 x 300
Primers Overlapping?No

Repertoire Publications

Publications associated with this study.

PubMed IDTitleAuthors
30733445Mosaic deletion patterns of the human antibody heavy chain gene locus shown by Bayesian haplotyping.Gidoni M, Snir O, Peres A, Polak P, Lindeman I, Mikocziova I, Sarna VK, Lundin KEA, Clouser C, Vigneault F, Collins AM, Sollid LM, Yaari G

Sequences of the PCR primers used in the study.

3' Primers

As the protocol used was 5’ RACE, there is only one primer set.

Primer NamePrimer Sequence
Human-IGHMGAATTCTCACAGGAGACGAGG
Human-IGHDTGTCTGCACCCTGATATGATGG
Human-IGHAGGGTGCTGYMGAGGCTCAG
Human-IGHETTGCAGCAGCGGGTCAAGG
Human-IGHGCCAGGGGGAAGACSGATG
Human-IGKGACAGATGGTGCAGCCACAG
Human-IGLAGGGYGGGAACAGAGTGAC

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
 TiggerTigger1.0.0

Notes

OGRDB plots are attached for each genotype.

Attachment File Name
 P1_I29_S1_ogrdbplot.pdf
 P1_I42_S1_ogrdbplot.pdf
 P1_I46_S1_ogrdbplot.pdf
 P1_I49_S1_ogrdbplot.pdf
 P1_I50_S1_ogrdbplot.pdf
 P1_I80_S1_ogrdbplot.pdf
 P1_I86_S1_ogrdbplot.pdf
 P1_I90_S1_ogrdbplot.pdf