High Resolution HLA Typing by Next Generation Exome Sequencing

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4166-4166 ◽  
Author(s):  
Chang Liu ◽  
Yang Xiao ◽  
Brian Duffy ◽  
Michael Zody ◽  
Eric Tycksen ◽  
...  

Abstract Abstract 4166 Background High resolution typing of HLA-A, B, C, DQB1 and DRB1 at the allelic level allows transplantation of hematopoietic progenitor cells (HPC) from matched allogeneic donors. The extent of matching has been recognized as one of the most important predictors of survival. High resolution typing relies on Sanger sequence-based typing (SBT) and PCR with sequence-specific primers (SSP), both of which detect nucleotide changes in exons that alter the HLA antigens. Next generation exome sequencing (NGES) offers the potential for rapid and less expensive HLA typing for transplantation of matched allogeneic HPC, but the role of NGES for high resolution HLA typing has not been examined. In this study, we designed a bioinformatic pipeline to account for the hundreds to thousands of alleles at each HLA locus in the population, and used it to explore the possibility of high resolution HLA typing using NGES data. Methods Indexed sequencing libraries were constructed from 3 HapMap samples (NA19129, NA18507, and NA19240), target enriched with SureSelect Human All Exon V3 kit (Agilent Technologies), and sequenced in multiplex as paired-end 2×101 bp reads on an Illumina HiSeq2000. The above process was repeated for NA19240 to assure reproducibility. The NGES-based HLA typing consisted of 3 major steps: 1) Filtering reads: cDNA and genomic sequences of all alleles of each HLA locus [ImMunoGeneTics project (IMGT)/HLA database] were concatenated to form five references, to which input reads were aligned using NovoalignMPI V.2.07.07 with standard options and no more than 1 mismatch per read. 2) Eliminating unsupported alleles: Curated alignment of all alleles of each HLA locus was obtained from IMGT/HLA database. Each polymorphic position was termed a D position. K-mers (a DNA sequence with length k), each containing a D position, was searched against the reads from step 1. Alleles were credited or penalized based on presence or absence of their k-mers in the reads. Alleles with negative overall scores were eliminated and this step was repeated until no elimination occurred. 3) Ranking allele pairs: all possible pairs of candidate alleles from step 2 were evaluated; a pair was credited at each D position if k-mers of both alleles were supported by the reads or penalized if otherwise. The allele pair (or pairs if a tie) ranked at the top was the presumed type of the locus examined. The NGES-based high resolution typing was run on a computing node (IBM x3650-m2). The results were compared with the results of conventional typing (SBT and SSP), followed by examination of the disagreement between the methods and adjustment of k. Results The conventional high resolution typing results comprised 15 pairs of alleles that were uniquely different (one pair of alleles at each locus of HLA-A, B, C, DQB1 and DRB1 for 3 samples). The method was established using the information on HLA-A alleles of NA19129, leaving 14 pairs of alleles for validation. Initial NGES-based typing indicated that the specificity of the method was dependent on k-mer length, with increased length required to eliminate interference from mimicking reads (e.g. mimics of an HLA-C allele). Thus, with a k-mer length of 50 bp, NGES-based typing correctly determined 12 of 14 pairs of alleles, while with k-mer lengths of 60 or 65 bp, it correctly determined 14 of 14 pairs of alleles. All 5 pairs of alleles of NA19240 were also correctly determined with the longer k-mers using reads from the replicate sequencing. After read filtering, the typing took approximately 5 minutes per sample. Conclusion In this first proof-of-concept study, high resolution HLA typing was successfully performed using NGES data. With k-mer lengths of 60 or 65 bp, NGES-based typing correctly identified 100% of tested allele pairs, and demonstrated a similar level of resolution and accuracy as conventional high resolution typing. Note: C.L. and X.Y. contributed equally to this work. Disclosures: No relevant conflicts of interest to declare.

Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1237-1237
Author(s):  
Marco Aurelio Salvino ◽  
Larissa A Medeiros ◽  
Alessandro Moura ◽  
Marianna Batista ◽  
Marilda Souza Goncalves ◽  
...  

Abstract Introduction Aplastic anemia (AA) is perceived as an immune mediated disease where T-lymphocytes recognize and destroy bone marrow elements leading to varying degrees of failure of hematopoiesis. Many autoimmune diseases have been linked to certain HLA alleles and such a relationship has been also been reported in AA. Expansion of CD8+ oligoclones has been reported in AA and likely contributes to pathogenesis. However, the interaction of CD4+ and CD8+ T cells and their targets mediated by human leukocyte antigen (HLA) class I and II peptides remain elusive. Thus, it has been speculated that polymorphic loci of these genes could be implicated in the susceptibility to the disease. Various alleles and haplotypes of HLA molecules have been implicated in the predisposition of AA development. The influence of HLA has been studied in North America, European and Asian countries. Data from Latin America, where there is a large mixture of Hispanic, European, and African descendants, is still lacking. This study focuses on the association between HLA alleles in AA patients in different regions of Brazil with particular ethnic groups. Patients and methods From 2000 to 2013, all patients with a diagnosis of acquired AA in the Brazilian state of Bahia (BA) followed at the Federal University of Bahia Hospital/ Foundation Hemoba who tested the HLA typing were included, totaling 215 patients. In this northeast region there is a predominance of African descendant (25% white, 75% brown/black). The genes in the analysis included HLA A, B, DR and DQ. SPSS was used to statistical calculations. Qui-square test/Fisher test were using the p-value correction of Bonferroni (p significant <0,0016) for comparison of genetic varieties.The HLA of patients with acquired AA Bahia (n = 215) were compared to the control group (3680 healthy non-related bone marrow volunteers donors from Bahia). To address regional differences within the country we also analyzed the HLA of AA patients (n = 344) from the State of Paraná located in the southern portion of the country and is characterized by a diverse ethnic mixture (71.3% white and 27% black/brown). Thus, we compared the findings of HLA associated with acquired AA in the two states, Bahia (northeast region) and Parana( south region). Of those statistically associated with AA (p<0,0016), we considered HLA clinically relevant only those present in at least 10% of cases and/or controls. Results From the 559 AA patients analysed, 45,1% were women, and 54.9% were men.The mean age was 23.4 (± 12.3). Among the HLA antigens with OR of risk or protection only HLA DR15 and B15, were significant, respectively (in both populations: Bahia and Parana). Identified as a risk factor for development of AA, HLA DR15 was found in 41.6% of patients (Bahia) versus 24% in controls (OR: 2.23 - CI: 1.68 to 2.9) (p <0.0001). As protective factor for AA development the HLA B15 was found in only 6% of patients (Bahia) versus 21.3% of controls (OR: 0.213, CI 0.12 to 0.370) (p <0.0001). A stratified analysis was conducted to assess the presence of interaction between the antigens DR15 and B15 in AA patients. When analyzing synergistically, the effects of HLA DR15 and B15, we observed that, in the AA group, the positivity of DR15+ of 41,6% falls significantly to 14,8%, when concurrently with the presence of B15+. The AA risk factor of HLA DR15+ loses its statistical risk power in presence of B15+. The incidence of B15+ patients (6% in AA patients) falls to 4% in the presence of DR15 negativity (p=ns). Conclusion We observed in 2 large AA cohorts (totaling 559 patients) from very distinct ethnic regions of Brazil, that, in both, HLA DR15 positivity was associated with a higher risk of disease, while B15 positivity was associated with a lesser likelihood of developing AA. The synergic combination of these alleles appears to be further associated with AA development. New studies analyzing synergic effect between HLA antigens/alleles should be conducted in immuno-mediated diseases. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 1524-1524
Author(s):  
Roisin Dunwoody ◽  
Richard Szydlo ◽  
Linda Casey ◽  
John Davis ◽  
Susan LLoyd ◽  
...  

Abstract Abstract 1524 The websites of the WMDA and BMDW list almost 100 registries providing volunteer unrelated donor (VUD) stem cells to the transplant community. A minority of these registries have completed a formal accreditation process although the majority of donors (>80%) in BMDW are contained within WMDA accredited registries. As a user of these registry services we were interested to assess variations in the efficiency of services in order to optimise our own search process and maximise our ability to transplant patients who might benefit in a timely manner. Within a national health service we are careful to contain costs and are aware that not only does the level of HLA typing of individual donors differ between registries but the costs of, and time to, obtaining confirmatory samples and the costs of eventual stem cell procurement also vary considerably. Since January 2004 we have maintained a comprehensive database to follow the progress of VUD searches in our institution. During this time searches were commenced for 193 patients (139 Caucasian, 15 African-Caribbean, 24 Asian and 15 mixed-race), and donors identified for 149 (77%). After high resolution typing of the potential recipient our initial request goes to our national hub which then provides a list of possible donors worldwide, including known degree of match and registry source. The simple parameter of time to donor identification is heavily influenced by the transplant centre which often categorises recipients in degrees of urgency and was not thought to be a useful measure of efficiency. Instead we looked at the availability of, time to obtain, and value of (as defined by degree of matching), confirmatory tissue typing samples once the request had been initiated, in addition to normal measures of the quality of the received stem cell product. For the 193 patients we requested further samples from 1226 donors with a median number of requests per patient of 7 (range 1–20). We utilised 30 registries (median number of requests per registry (R/R) of 3, range 1–387), although some 50% of the requests went to only 5 registries with a median of 220 R/R, range 43–387. 806 confirmatory samples were received from 1226 requests (66%). Donor availability and the time to sample arrival were compared in the 5 most frequently utilised registries, hereafter known as registries A-E. The percentage of the requests that resulted in samples and the percentages of samples found to be HLA-matched were 76%, 72%, 70%, 67% and 53% and 31%, 41%, 40%, 46% and 28% from registries A,B,C,D and E respectively. The chance of obtaining a suitable HLA-matched donor was highest from registry D at 31% and lowest from registry E at 15%. Failure to supply a confirmatory sample is due to inability to contact the donor, temporary unavailability or donor refusal and was unacceptably high in registry E at 47%. The median times from request to sample arrival ranged from 15–22 days. We confirmed the difficulties in finding donors for non-Caucasian patients with fewer potential donors provided initially by our hub and a reduced chance of finding fully HLA matched donors (defined generously as 8/8 antigens matched). Such donors were found for 62%, 26%, 46% and 40% of Caucasian, African-Caribbean, Asian and mixed-race patients. 61 patients have been transplanted to date. No differences were found between the 5 registries in the hours to infusion, viability at infusion, volume collected, total nucleated cell counts, CD34+cell numbers or time to engraftment. Of the 88 patients for whom donors were found but no transplant has been performed, 72 remain alive on treatment. Many of these have chronic myeloid leukemia (CML) and are responding to second generation tyrosine kinase inhibitors. The costs of obtaining samples varies from approximately $500-2000 per sample resulting in a range of 500 to several thousand dollars per patient. Cost cannot be recouped in our country if the transplant is not performed. As a result of this audit we have refined our search process using the initial search as a surrogate for the ease of finding a donor subsequently, so that full searches are only initiated in patients failing imatinib if they have few donors and/or donors with low resolution typing and focussing on those registries most likely to provide HLA-matched blood samples. Registries also have a responsibility to improve their service and minimise costs by focussing on donor retention and high resolution typing. Disclosures: No relevant conflicts of interest to declare.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 4880-4880
Author(s):  
Ching-Tien Peng

Abstract Congenital dyserythropoietic anemia (CDAs) is a group of hereditary disorders characterized by ineffective erythropoiesis and distinct morphological abnormalities of erythroblasts in the bone marrow. Diagnosis of CDA is based primarily on the morphology of bone marrow erythroblasts but genetic tests might have more and more important roles recently. Here, we describe a 31-year old female with atypical CDA under regular blood transfusions. The results of blood tests were as followed: RBC: 3080000/µL, Hb: 9.9 g/dL, Hct: 26.8%, MCV: 87.0 fl, MCH:32.2 pg, and MCHC: 36.9 g/L. In this study, analysis of CDA-related genes, including SEC23B, CDAN1, KLF1, and C15orf41, were analyzed by exome sequencing but no pathogenic variant was found. In additional, we analyzed RBC-related genes and a novel variant in the PKLR p.A468G (NP_000289) was found which was also confirmed by Sanger sequence. Variant of PKLR gene has been reported as the cause of pyruvate kinase (PK) deficiency anemia. PK deficiency is the most cause of congenital nonspherocytic hemolytic anemia with GMAF (global minor allele frequency) of 0.0001. The clinical features of PK-deficient patients are highly variable degree of chronic hemolysis with severe neonatal jaundice and fetal anemia at birth. In this case, PKLR p.A468G heterozygous variant was detected in a patient with PK deficiency, as an example of precision diagnosis by exome sequencing. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 3537-3537
Author(s):  
Stefan O. Ciurea ◽  
Rima M. Saliba ◽  
Gabriela Rondon ◽  
Poliana A. Patah ◽  
Morgani Rodrigues ◽  
...  

Abstract Abstract 3537 Donor-recipient HLA mismatches are associated with increased morbidity and mortality after UD hematopoietic stem cell transplants (HSCT). We hypothesized that HLA-DP mismatches would worsen outcomes of HSCT using donors mismatched at HLA-A,-B,-C,-DRB1 or -DQB1 and evaluated 391 consecutive patients (pts) with myeloid malignancies treated at our institution with 0,1,2,3 mismatches out of 12 alleles typed by high resolution at HLA-A,-B,-C,-DR,-DQ,-DP loci. Eighty-one pts were 12/12, 180 pts were 11/12, 113 pts were 10/12, and 15 pts were 9/12 HLA match with the recipients. Characteristics of the 4 groups (12/12, 11/12, 10/12, 9/12) were similar except source of stem cells; 87% of pts with 9/12 donors received bone marrow versus 60–62% for the other 3 groups. Results: Two-year overall survival (OS) and progression-free survival (PFS) were 40%, 44%, 45%, 53% and 33%, 40%, 44%, 49%, respectively (p=NS). However, OS was significantly worse with increasing number of mismatches for patients with AML/MDS with poor-risk cytogenetics (p=0.005, HR 1.6, 95% CI 2.1–4.2). Except for the 9/12 group, pts had a significantly higher non-relapse mortality (NRM) (11%, 24%, 36%) and lower risk of progression (32%, 25%, 20%). In the 9/12 group, NRM was 27% and progression rate was 40%. Grade II-IV, III-IV aGVHD as well as cGVHD were also progressively worse with increasing number of mismatches. Gr II-IV and III-IV aGVHD rates were 35%, 37%, 41%, 69%, and 8%, 8%, 15%, 16%, respectively. Cumulative incidence of cGVHD was 35%, 39%, 44% and 61%, respectively. Compared with 11–12/12 donors, pts who received a 9–10/12 donor had significantly higher rates of gr III-IV aGVHD and cGVHD (p=0.03, HR 2.1, CI 1.1–3.7 and p=0.02, HR 1.5, CI 1.1–2.1, respectively). Univariate analysis revealed that there is less NRM with a 12/12 donor (vs. other) (p=0.008, HR 1.9, 95% CI 1.2–2.9), while in multivariate analysis, compared with a 12/12 donor, the use of a donor with mismatch was significantly associated with higher NRM [HR and 95%CI were 2.1 and 1.04–4.4 for 11/12 donor (p=0.04); 3.1 and 1.5–3.3 for 10/12 donor (p=0.003); 2.8 and 0.9–9.3 for a 9/12 donor (p=0.08), respectively] (Figure). In multivariate analysis, factors significantly associated with OS were disease status at transplant (active disease vs. not) (p<0.001), cytogenetics for AML/MDS pts (poor-risk vs. other) (p=0.006, HR) and the use of fludarabine and busulfan conditioning (Bu 130mg/m2 × 4 days and Flu vs. other) (p=0.04, HR 0.7, CI 0.5–0.98), while factors significantly associated with NRM were, in addition to degree of mismatch, disease status at transplant (p=0.008, HR 1.9, CI 1.2–3.1) and use of BuFlu conditioning (p=0.004, HR 0.5, CI 0.4–0.8). In conclusion, these results suggest that, using 12/12 high-resolution HLA typing, a progressively higher NRM is encountered for unrelated donor pts with higher number of mismatches, at least in part related to higher rates of GVHD. Matching at DP loci appears to be protective of NRM and is associated with improved survival for patients with AML/MDS with poor-risk cytogenetics. Disclosures: No relevant conflicts of interest to declare.


2020 ◽  
Vol 11 ◽  
Author(s):  
Minh Duc Do ◽  
Linh Gia Hoang Le ◽  
Vinh The Nguyen ◽  
Tran Ngoc Dang ◽  
Nghia Hoai Nguyen ◽  
...  

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1394-1394
Author(s):  
Suning Chen ◽  
Nana Ping ◽  
Jia Yin ◽  
Wenxiu Cheng ◽  
Qinrong Wang ◽  
...  

Abstract Acute erythroid leukemia (AEL) is a distinct subtype of acute myeloid leukemia (AML) characterized by predominant erythropoiesis. Currently, only few studies using next-generation sequencing were reported in AEL. To decipher the somatic mutation spectrum and discover disease-driving genes responsible for the pathogenesis of AEL, we performed whole exome-sequencing (WES) in 6 AEL and validating using targeted next generation sequencing (NGS) and Sanger sequencing in 58 AEL. From August 2003 to October 2014, a total of 158 patients fulfilling the WHO criteria for AEL were identified, comprising 91 males and 67 females. Median age was 50 years. These patients were further subclassified into 3 groups: 37 AEL after MDS, 108 de novo AEL, and 13 AML with myelodysplasia-related changes. In total, we identified 52 genes with somatic mutations in at least 2 patients, including CEBPA in 4 patients and GATA2 in 2 patients. We identified high frequencies of mutations in CEBPA (40.0%, 22/55; about 1/4 are biallelic mutations), GATA2 (22.4%, 13/58), NPM1 (15.5%, 9/58), SETBP1 (12.1%, 7/58), and U2AF1 (12.1%, 7/58), followed by TP53 (5.2%, 3/58), RUNX1 (3.5%, 2/58), TET2 (3.5%,2/58), ASXL1 (3.5%, 2/58), DNMT3A (3.5%, 2/58), SRSF2 (1.7%, 1/58) and FLT3 (1.7%, 1/58). We did not detect alterations of some of commonly mutated genes associated with AML, including IDH1, IDH2 and RAS. The results are summarized in Figure 1. To further identify the prevalence of GATA2 mutations in hematologic malignancies, we amplified and sequenced the entire coding region of GATA2 gene in 253 non-AEL AML, 40 chronic myeloid leukemia in blast crisis (CML-BC), 55 B-cell acute lymphoblastic leukemia (B-ALL), and 38 T-cell acute lymphoblastic leukemia (T-ALL). We detected GATA2 mutations in 5.5% of non-AEL AML, 15% of CML-BC, and none of B-ALL or T-ALL. The GATA2 mutations in AEL are mainly localized in ZF1 domain (P304H, D309E, A318V/T, G320S/D, L321P, and R330X) and TAD domain (Q20H). To find out the implications of GATA2 mutations in the leukemogenesis of AEL, we overexpressed the mutants of GATA2 (P304H, L321P, and R330X) in 293T cells and demonstrate that GATA2 mutant led to reduced transcriptional activity. Whereas overexpression of GATA2 mutants in mouse myeloid progenitor cell line, 32D, has no effect on the proliferative or colony formation abilities, it caused increased expression of erythroid-related antigen Ter-119 (Figure 2), b-globin and bh1-globin. Furthermore, 32D cells transfected with GATA2 mutants showed increased positivity than control cells by Benzidine staining. Taken together, our findings demonstrate that the mutatome of AEL is different from other types of AML. AEL is associated with a high frequency of mutations in GATA2 and CEBPA. GATA2 mutations resulted in a decrease of transcriptional activity and erythroid development of mouse myeloid progenitors, suggest an important role of GATA2 mutations in AEL. Figure 1. Figure 1. Figure 2. Figure 2. Disclosures No relevant conflicts of interest to declare.


2018 ◽  
Vol 31 (Supplement_1) ◽  
pp. 51-51
Author(s):  
Máté Csucska ◽  
Balázs Kovács ◽  
Lilla Ozorai ◽  
Árpád Patai ◽  
Zoltán Lóderer ◽  
...  

Abstract Background Fundoplication is a well accepted method in treatment of gastro-esophageal reflux disease. High Resolution Manometry (HRM) is essential in diagnosis of functional esophageal diseases. The aim of our study was to find the place and value of HRM after 6 months of Toupet-fundoplication, and find correlation in symptoms remained, if any. Methods In 2016–2017 98 Toupet-fundoplications were performed by single surgeon. Surgeries were after HRM, EGD and pre-operative reflux symptom questionnaire performed in our Esophageal Center. Six months after surgery EGD, HRM and post-operative symptom questionnaire was planned to manage in each patients. Results Until Feb/01/2018 74/98 patients were more than 6 months after their operation. 72/74 patients completed the questionnaire and the EGD as well. 28/72 patients absolved HRM also. 25/28 patients had no complains and pre-operative symptoms relieved completely requiring neither PPI nor H2 blockers. 2/28 patients had gastric emptying problems, and 1/28 had moderate reflux associated symptom. Compared to that 22/28 patients HRM verified abnormal values mostly in DCI, however these 22 patients were asymptomatic. It has to be mentioned that DCI was better pre-operatively than post-operatively in 12 out of 22 cases. Conclusion Post-operative HRM can qualify and describe the wrap objectively (its location and basic pressure) however the latest Chicago-criteria was not developed for after-surgery states. We can conclude that post-operative routine HRM can mislead the physician, has importance only in patients with significant complains. Disclosure All authors have declared no conflicts of interest.


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