Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population

Creary, Lisa E.; Gangavarapu, Sridevi; Mallempati, Kalyan C.; Montero‐Martin, Gonzalo; Caillier, Stacy J.; Santaniello, Adam; Hollenbach, Jill A.; Oksenberg, Jorge R.; Fernández-Viña, Marcelo

doi:10.1016/j.humimm.2019.07.275

Cited by 41 publications

(46 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Detailed analysis of the units containing this LD showed that others LD for HLA-DRB1~HLA-DQB1 are more likely to be present, since they have been previously reported (Suppl. Table 7 ) 27 – 33 .…”

Section: Resultsmentioning

confidence: 99%

HLA diversity in the Argentinian Umbilical Cord Blood Bank: frequencies according to donor’s reported ancestry and geographical distribution

Souto

Rosello

Lazo

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Umbilical cord blood (UCB) is a suitable source for hematopoietic stem cell transplantation. The study of HLA genes by next generation sequencing is commonly used in transplants. Donor/patient HLA matching is often higher within groups of common ancestry, however “Hispanic” is a broad category that fails to represent Argentina’s complex genetic admixture. Our aim is to describe HLA diversity of banked UCB units collected across the country taking into consideration donor’s reported ancestral origins as well as geographic distribution. Our results showed an evenly distribution of units mainly for 2 groups: of European and of Native American descent, each associated to a defined geographic location pattern (Central vs. North regions). We observed differences in allele frequency distributions for some alleles previously described in Amerindian populations: for Class I (A*68:17, A*02:11:01G, A*02:22:01G, B*39:05:01, B*35:21, B*40:04, B*15:04:01G, B*35:04:01, B*51:13:01) and Class II (DRB1*04:11:01, DRB1*04:07:01G/03, DRB1*08:02:01, DRB1*08:07, DRB1*09:01:02G, DRB1*14:02:01, DRB1*16:02:01G). Our database expands the current knowledge of HLA diversity in Argentinian population. Although further studies are necessary to fully comprehend HLA heterogeneity, this report should prove useful to increase the possibility of finding compatible donors for successful allogeneic transplant and to improve recruitment strategies for UCB donors across the country.

show abstract

Section: Resultsmentioning

confidence: 99%

HLA diversity in the Argentinian Umbilical Cord Blood Bank: frequencies according to donor’s reported ancestry and geographical distribution

Souto

Rosello

Lazo

et al. 2021

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The population founder effect can lead to reduced genetic diversity and altered frequencies of genetic variants (Chheda et al 2017), including HLA alleles and haplotypes (Hurley et al 2020; Creary et al 2019). The current study was based on a genetically defined cohort of Finnish individuals that constitutes a Northern European genetic isolate.…”

Section: Discussionmentioning

confidence: 99%

Phenome-wide HLA association landscape of 235,000 Finnish biobank participants

Ritari

Koskela

Hyvärinen

et al. 2020

Preprint

View full text Add to dashboard Cite

The human leukocyte antigen (HLA) system is the single most important genetic susceptibility factor for many autoimmune diseases and immunological traits. However, in a range of clinical phenotypes the impact of HLA alleles or their combinations on disease risk is not comprehensively understood. For systematic population-level analysis of HLA-phenotype associations we imputed the alleles of classical HLA genes in a discovery cohort of 146,630 and a replication cohort of 89,340 Finnish individuals for whom SNP genotype data and 3,355 disease phenotypes were available as part of the FinnGen project. In total, 3,649 significant single HLA allele associations in 368 phenotypes were found in both cohorts. In addition to known susceptibility alleles, we discovered a number of previously poorly established HLA associations. For example, DRB1*04:01-DQB1*03:02, a frequent high-risk haplotype for many autoimmune diseases, was also independently associated with infectious diseases. Conditional analyses to distinguish protective effects from nonpredisposition showed that in 21 disease categories the effect of the high-risk allele was significantly decreased by a heterozygoous allele in the same locus. Furthermore, in many immunological diseases the strength of the top risk-allele was significantly modified by an HLA gene of a different class. The results highlight the complex structure of HLA-disease associations and suggest that the entire HLA composition should be considered in genetic risk estimation and functional studies. Independent cross-phenotype HLA class II associations imply pleiotropic effects particularly with autoimmune and infectious diseases, supporting a link between environmental exposure and immunogenetics in these diseases.

show abstract

“…The library was then sequenced on an Illumina MiSeq Next Generation Sequencer at the Stanford Functional Genomics Facility. HLA typing was performed by extended/full gene next-generation sequencing as described previously (37). EBV genome sequence analysis.…”

Section: Methodsmentioning

confidence: 99%

Genomic variations in EBNA3C of EBV associate with posttransplant lymphoproliferative disorder

Maloney¹,

Busque²,

Hui³

et al. 2020

JCI Insight

View full text Add to dashboard Cite

Next-generation sequencing reveals new information about HLA allele and haplotype diversity in a large European American population

Cited by 41 publications

References 56 publications

HLA diversity in the Argentinian Umbilical Cord Blood Bank: frequencies according to donor’s reported ancestry and geographical distribution

HLA diversity in the Argentinian Umbilical Cord Blood Bank: frequencies according to donor’s reported ancestry and geographical distribution

Phenome-wide HLA association landscape of 235,000 Finnish biobank participants

Genomic variations in EBNA3C of EBV associate with posttransplant lymphoproliferative disorder

Contact Info

Product

Resources

About