Papers by Jill Hollenbach
Aim Recent data show that DP matching plays an important role in hematopoietic cell transplantati... more Aim Recent data show that DP matching plays an important role in hematopoietic cell transplantation. Our previous work demonstrated that in European Americans haplotypic associations for the DP heterodimer are determined by near complete linkage disequilibrium between amino acid motifs on DPA1 (pos 31) and DPB1 (pos 85–87). We aimed to generate motif and allele-level haplotype frequencies (HF) for four race groups to extend these insights to minorities. Methods We calculated DPA1∼DPB1 HF at allele and motif level from 16,802 Be the Match Registry® members typed by DNA methods, resolving phase, allelic and motif ambiguity using expectation maximization. Motif frequencies were calculated for position 31 on DPA1 and positions 85–87 on DPB1, which play a critical role in the P1 pocket of the peptide binding region. Normalized linkage disequilibrium (LD) was calculated on each haplotype (D′) and globally (Wn) for each population. Results The top three allele-level haplotypes in all popul...
Bookmarks Related papers MentionsView impact
Bookmarks Related papers MentionsView impact
Bookmarks Related papers MentionsView impact
Bookmarks Related papers MentionsView impact
Bookmarks Related papers MentionsView impact
Immunogenetics, 2014
HLA class I molecules and killer cell immunoglobulin-like receptors (KIR) form a diverse system o... more HLA class I molecules and killer cell immunoglobulin-like receptors (KIR) form a diverse system of ligands and receptors that individualize human immune systems in ways that improve the survival of individuals and populations. Human settlement of Oceania by island-hopping East and Southeast Asian migrants started ~3,500 years ago. Subsequently, New Zealand was reached ~750 years ago by ancestral Māori. To examine how this history impacted KIR and HLA diversity, and their functional interaction, we defined at high resolution the allelic and haplotype diversity of the 13 expressed KIR genes in 49 Māori and 34 Polynesians. Eighty KIR variants, including four 'new' alleles, were defined, as were 35 centromeric and 22 telomeric KIR region haplotypes, which combine to give >50 full-length KIR haplotypes. Two new and divergent variant KIR form part of a telomeric KIR haplotype, which appears derived from Papua New Guinea and was probably obtained by the Asian migrants en route t...
Bookmarks Related papers MentionsView impact
PLoS Genetics, 2013
Bookmarks Related papers MentionsView impact
Human immunology, 2015
Multiple lines of evidence support an immunologic basis and genetic disposition for the developme... more Multiple lines of evidence support an immunologic basis and genetic disposition for the development of age-related macular degeneration (AMD). Comprehensive human leukocyte antigens (HLA) class II typing at four loci (DRB1, DQA1, DQB1, and DPB1) was assessed using next generation sequencing methods and tested for association with age-related macular degeneration (AMD) in a case-control study of 456 AMD cases and 499 controls from the population-based Study of Osteoporotic Fractures (SOF) cohort. No statistically significant associations were identified for any of the class II loci and a previously identified association between DRB1*13:01 was not replicated in this dataset. These results reported here suggest that common HLA class II genetic variation does not contribute to AMD disease risk.
Bookmarks Related papers MentionsView impact
Biocomputing 2010, 2009
Bookmarks Related papers MentionsView impact
PLoS ONE, 2012
Bookmarks Related papers MentionsView impact
International Journal of Immunogenetics, 2012
The goal of the immunogenomic data analysis working group (IDAWG) is to facilitate the consistent... more The goal of the immunogenomic data analysis working group (IDAWG) is to facilitate the consistent analysis of HLA and KIR data, and the sharing of those data among the immunogenomic and larger genomic communities. However, the data management approaches currently applied by immunogenomic researchers are not widely discussed or reported in the literature, and the effect of different approaches on data analyses is not known. With ASHI's support, the IDAWG developed a 45 question survey on HLA and KIR data generation, data management and data analysis practices. Survey questions detailed the loci genotyped, typing systems used, nomenclature versions reported, computer operating systems and software used to manage and transmit data, the approaches applied to resolve HLA ambiguity and the methods used for basic population-level analyses. Respondents were invited to demonstrate their HLA ambiguity resolution approaches in simulated data sets. By May 2012, 156 respondents from 35 nations had completed the survey. These survey respondents represent a broad sampling of the Immunogenomic community; 52% were European, 30% North American, 10% Asian, 4% South American and 4% from the Pacific. The project will continue in conjunction with the 17th Workshop, with the aim of developing community data sharing standards, ambiguity resolution documentation formats, single-task data Management tools and novel data analysis methods and applications. While additional project details and plans for the 17th IHIW will be forthcoming, we welcome the input and participation in these projects from the histocompatibility and immunogenetics community.
Bookmarks Related papers MentionsView impact
Immunogenetics, 2009
Bookmarks Related papers MentionsView impact
Immunogenetics, 2012
Bookmarks Related papers MentionsView impact
Human Immunology, 2009
Bookmarks Related papers MentionsView impact
Human Immunology, 2009
Bookmarks Related papers MentionsView impact
Human Immunology, 2012
ABSTRACT Aim A ‘Silver Standard’ for HLA data collection and reporting has been described at ImmP... more ABSTRACT Aim A ‘Silver Standard’ for HLA data collection and reporting has been described at ImmPort (immport.niaid.nih.gov, “Proposal for HLA Data Validation”) to address ambiguity resolution in the recording and reporting of HLA typing results. While standards are critical for HLA data interoperability, they are not meaningful until useful tools are developed and made available for community use. We are developing distributable tools that implement this silver standard. Here we describe the development a web service to create, update, and retrieve HLA typing data in standardized formats without the need for NMDP allele codes and the corresponding inherent introduction of new ambiguities. Methods ReST web services with HTTP negotiation are being developed employing a Java library that manages HLA typing data using standardized formats. These formats include the XML based Histoimmunogenetics Markup Language (HML) and a simple character-delimited string format (GL String) able to encode ambiguity within HLA typing. Resources are identified with a simple Uniform Resource Identifier (URI). Results The services build on a foundation of an open access database schema for IMGT/HLA reference sequence data (updated quarterly), and objects such as alleles, lists of alleles, haplotypes, genotypes, lists of genotypes and multi-locus unphased genotypes. Public services include creating, updating, and retrieving these objects. Content negotiation allows data retrieval in a variety of formats including GL String, HML, HTML, JSON, and QR Code. Conclusions The tools being developed here provide the HLA researcher, clinician and lab technician a common resource for managing HLA data in a standardized way. We envision these tools to augment workflows through creating new instances of HLA typing objects when needed, and retrieval of those objects and their associated metadata when called upon.
Bookmarks Related papers MentionsView impact
Arthritis & Rheumatism, 2010
Bookmarks Related papers MentionsView impact
immport.net
A. History B. Estimating allele frequencies: the method of gene (allele) counting C. The variance... more A. History B. Estimating allele frequencies: the method of gene (allele) counting C. The variance of the allele frequency estimates D. Derivation of Hardy-Weinberg proportions (HWP) E. Evolutionary implications of HW F. Two extreme examples showing fit and lack of fit to HWP G. Hardy-Weinberg equilibrium for an X-linked trait H. Estimation of allele frequency and carrier frequency for a recessive trait
Bookmarks Related papers MentionsView impact
immport.org, 2011
LD—linkage disequilibrium; LE—linkage equilibrium; n—# of individuals in a sample; NK—Natural Kil... more LD—linkage disequilibrium; LE—linkage equilibrium; n—# of individuals in a sample; NK—Natural Killer PyPop—www. pypop. org, www. ImmPort. org (Python for Population Genomics–PyPop, current release version 0.7. 0)(Lancaster et al. 2003, 2007a, 2007b, 2008; Lancaster 2006); r—the correlation coefficient between the allele frequency distributions at two bi-allelic loci denoted A and B, with r 2= D 2/[pA1pA2pB1pB2]; SIRE—self identified race/ethnicity Wn—also denoted WAB, the multi-allelic extension of the bi- ...
Bookmarks Related papers MentionsView impact
Tissue antigens, 2014
Genetic matching for loci in the human leukocyte antigen (HLA) region between a donor and a patie... more Genetic matching for loci in the human leukocyte antigen (HLA) region between a donor and a patient in hematopoietic stem cell transplantation (HSCT) is critical to outcome; however, methods for HLA genotyping of donors in unrelated stem cell registries often yield results with allelic and phase ambiguity and/or do not query all clinically relevant loci. We present and evaluate a statistical method for in silico imputation of HLA alleles and haplotypes in large ambiguous population data from the Be The Match(®) Registry. Our method builds on haplotype frequencies estimated from registry populations and exploits patterns of linkage disequilibrium (LD) across HLA haplotypes to infer high resolution HLA assignments. We performed validation on simulated and real population data from the Registry with non-trivial ambiguity content. While real population datasets caused some predictions to deviate from expectation, validations still showed high percent recall for imputed results with aver...
Bookmarks Related papers MentionsView impact
Uploads
Papers by Jill Hollenbach