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Nunes K, Maia MHT, Dos Santos EJM, Dos Santos SEB, Guerreiro JF, Petzl-Erler ML, Bedoya G, Gallo C, Poletti G, Llop E, Tsuneto L, Bortolini MC, Rothhammer F, Single R, Ruiz-Linares A, Rocha J, Meyer D. How natural selection shapes genetic differentiation in the MHC region: A case study with Native Americans. Hum Immunol 2021; 82:523-531. [PMID: 33812704 PMCID: PMC8217218 DOI: 10.1016/j.humimm.2021.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 02/15/2021] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
The Human Leukocyte Antigen (HLA) loci are extremely well documented targets of balancing selection, yet few studies have explored how selection affects population differentiation at these loci. In the present study we investigate genetic differentiation at HLA genes by comparing differentiation at microsatellites distributed genomewide to those in the MHC region. Our study uses a sample of 494 individuals from 30 human populations, 28 of which are Native Americans, all of whom were typed for genomewide and MHC region microsatellites. We find greater differentiation in the MHC than in the remainder of the genome (FST-MHC = 0.130 and FST-Genomic = 0.087), and use a permutation approach to show that this difference is statistically significant, and not accounted for by confounding factors. This finding lies in the opposite direction to the expectation that balancing selection reduces population differentiation. We interpret our findings as evidence that selection favors different sets of alleles in distinct localities, leading to increased differentiation. Thus, balancing selection at HLA genes simultaneously increases intra-population polymorphism and inter-population differentiation in Native Americans.
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Affiliation(s)
- Kelly Nunes
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil.
| | | | | | | | | | | | - Gabriel Bedoya
- Instituto de Biología, Universidad de Antioquia, Medellín, Colombia
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Giovanni Poletti
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Elena Llop
- Instituto de Ciencias Biomédicas, Faculdad de Medicina, Universidade de Chile, Santiago, Chile
| | - Luiza Tsuneto
- Departamento de Ciências Básicas da Saúde, Universidade Estadual de Maringá, Maringá, Brazil
| | - Maria Cátira Bortolini
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | | | - Richard Single
- Department of Mathematics and Statistics, University of Vermont, Burlington, VT, USA
| | - Andrés Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200433, China; D Aix-Marseille University, CNRS, EFS, ADES, Marseille 13007, France
| | - Jorge Rocha
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal; CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal.
| | - Diogo Meyer
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, Brazil.
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Fernandez Vina MA, Hollenbach JA, Lyke KE, Sztein MB, Maiers M, Klitz W, Cano P, Mack S, Single R, Brautbar C, Israel S, Raimondi E, Khoriaty E, Inati A, Andreani M, Testi M, Moraes ME, Thomson G, Stastny P, Cao K. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations. Philos Trans R Soc Lond B Biol Sci 2012; 367:820-9. [PMID: 22312049 DOI: 10.1098/rstb.2011.0320] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans.
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Aiello Bowles EJ, Feigelson HS, Barney T, Broecker K, Sterrett A, Bischoff K, Engel J, Gundersen G, Sheehey-Jones J, Single R, Onitilo A, James TA, McCahill LE. Improving quality of breast cancer surgery through development of a national breast cancer surgical outcomes (BRCASO) research database. BMC Cancer 2012; 12:136. [PMID: 22472011 PMCID: PMC3350402 DOI: 10.1186/1471-2407-12-136] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 04/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Common measures of surgical quality are 30-day morbidity and mortality, which poorly describe breast cancer surgical quality with extremely low morbidity and mortality rates. Several national quality programs have collected additional surgical quality measures; however, program participation is voluntary and results may not be generalizable to all surgeons. We developed the Breast Cancer Surgical Outcomes (BRCASO) database to capture meaningful breast cancer surgical quality measures among a non-voluntary sample, and study variation in these measures across providers, facilities, and health plans. This paper describes our study protocol, data collection methods, and summarizes the strengths and limitations of these data. METHODS We included 4524 women ≥18 years diagnosed with breast cancer between 2003-2008. All women with initial breast cancer surgery performed by a surgeon employed at the University of Vermont or three Cancer Research Network (CRN) health plans were eligible for inclusion. From the CRN institutions, we collected electronic administrative data including tumor registry information, Current Procedure Terminology codes for breast cancer surgeries, surgeons, surgical facilities, and patient demographics. We supplemented electronic data with medical record abstraction to collect additional pathology and surgery detail. All data were manually abstracted at the University of Vermont. RESULTS The CRN institutions pre-filled 30% (22 out of 72) of elements using electronic data. The remaining elements, including detailed pathology margin status and breast and lymph node surgeries, required chart abstraction. The mean age was 61 years (range 20-98 years); 70% of women were diagnosed with invasive ductal carcinoma, 20% with ductal carcinoma in situ, and 10% with invasive lobular carcinoma. CONCLUSIONS The BRCASO database is one of the largest, multi-site research resources of meaningful breast cancer surgical quality data in the United States. Assembling data from electronic administrative databases and manual chart review balanced efficiency with high-quality, unbiased data collection. Using the BRCASO database, we will evaluate surgical quality measures including mastectomy rates, positive margin rates, and partial mastectomy re-excision rates among a diverse, non-voluntary population of patients, providers, and facilities.
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Affiliation(s)
- Erin J Aiello Bowles
- Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA.
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McCahill LE, Single R, Ratliff J, Sheehey-Jones J, Gray A, James T. Local recurrence after partial mastectomy: relation to initial surgical margins. Am J Surg 2011; 201:374-8;discussion 378. [PMID: 21367382 DOI: 10.1016/j.amjsurg.2010.09.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2010] [Revised: 09/08/2010] [Accepted: 09/13/2010] [Indexed: 11/25/2022]
Abstract
BACKGROUND Local recurrence (LR) after partial mastectomy (PM) has been associated with inadequate surgical margins. We assessed LR association with initial margins after PM in patients receiving postoperative radiation therapy (RT). METHODS Initial margins, re-excision status, and ipsilateral LR were identified for all patients having initial PM from 2003 to 2008. RESULTS Seven hundred twelve patients underwent PM as their final procedure, and 598 (84.0%) had adjuvant RT. Initial margins were positive or <1-mm margins in 166 patients (27.8%). Re-excision was performed for all positive and 20.2% of patients with margins <1 mm. We observed 10 LRs (1.7%) at the 3.4-year mean follow-up. For patients with initial margins <1 mm, the LR rate was 4.2% (7/167) and just .7% for margins ≥1 mm (P = .006). CONCLUSIONS We report lower LR rates than traditionally reported. The surgical practice of re-excision to achieve margins of 1 to 5 mm needs closer scrutiny because it may have no impact on LR.
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Affiliation(s)
- Laurence E McCahill
- Richard J. Lacks Cancer Center, Saint Mary's Health Care, Grand Rapids, MI 49503, USA.
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Guidry P, Marthandan N, Smith T, Campbell J, Dunn P, Erlich H, Karp D, Single R, Thomson G, Wiser J, Scheuermann R, Mack S. An HLA allele frequency-based approach to resolving allelic and genotypic ambiguity in HLA typing data and its implementation in ImmPort (65.22). The Journal of Immunology 2011. [DOI: 10.4049/jimmunol.186.supp.65.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
The classical human leukocyte antigen (HLA) loci are the most polymorphic loci in the human genome, with hundreds of new alleles reported yearly. HLA polymorphisms in exons 2 and 3 of class I loci and in exon 2 of class II loci distinguish the peptide binding regions of HLA proteins. Current HLA typing methodologies focus on identifying variant positions in these exons, and most do not detect allelic variation in other exons or non-coding regions of HLA genes. Because of the limitations in detecting polymorphic variants and the pace of new allele discovery, commonly used HLA typing methodologies cannot unambiguously identify all known HLA alleles or genotypes. Consequently, many HLA genotyping results are ambiguous in that both alleles of each HLA locus for a given subject may have multiple possible identities, and each subject may have multiple possible genotypes. Here, we describe an approach to allelic and genotypic ambiguity resolution that uses published HLA allele frequencies in 10 world regions to determine the most likely diploid alleles and genotype for each subject in an HLA typing study. This method has been implemented in an online tool at www.ImmPort.org, and is freely available for use by the immunology community. This ambiguity reduction tool will allow investigators studying autoimmune disease, adverse drug reactions, transplantation outcome and other HLA associated conditions to more accurately determine the contribution of specific HLA alleles to disease.
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Affiliation(s)
- Paula Guidry
- 1Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Nishanth Marthandan
- 1Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Thomas Smith
- 2Health Information Systems, Northrop Grumman, Inc., Rockville, MD
| | - John Campbell
- 2Health Information Systems, Northrop Grumman, Inc., Rockville, MD
| | - Patrick Dunn
- 2Health Information Systems, Northrop Grumman, Inc., Rockville, MD
| | - Henry Erlich
- 3Children’s Hospital Oakland Research Institute, Oakland, CA
- 4Department of Human Genetics, Roche Molecular Systems, Inc., Alameda, CA
| | - David Karp
- 5Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX
| | - Richard Single
- 6Department of Mathematics and Statistics, University of Vermont, Burlington, VT
| | - Glenys Thomson
- 7Department of Integrative Biology, University of California, Berkeley, CA
| | - Jeffrey Wiser
- 2Health Information Systems, Northrop Grumman, Inc., Rockville, MD
| | - Richard Scheuermann
- 1Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
- 8Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX
| | - Steven Mack
- 3Children’s Hospital Oakland Research Institute, Oakland, CA
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James T, McCahill L, Ratliff J, Ashikaga T, Single R, Sheehey-Jones J, Messier N, Stanley M, Krag D, Harlow S. Quality assessment of neoadjuvant therapy use in breast conservation: barriers to implementation. Breast J 2009; 15:524-6. [PMID: 19624412 DOI: 10.1111/j.1524-4741.2009.00771.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Neoadjuvant systemic therapy (NST) for operable breast cancer can increase the options for conservative surgery in patients with breast cancer. We performed an analysis of a breast cancer outcomes database as a quality assessment of neoadjuvant therapy use in relation to breast conservative rate (BCR). Data were reviewed from a breast cancer database established to monitor outcomes of breast cancer surgery at a tertiary care breast cancer clinic. The frequency of NST-use was correlated to tumor size and BCR. Cause-specific factors for omitting NST in patients undergoing mastectomy for tumors 3 cm or greater were determined. NST was employed in 29 of 241 (12%) cases of invasive breast carcinoma treated surgically from 2003 to 2005. Although a significant decrease in BCR occurred in tumors >3 cm, NST was not frequently employed until tumors reached >5 cm. Defined contraindications to breast conservation (65%) and patient choice for mastectomy (30%) were the two most common reasons for omitting NST in tumors > or = 3 cm. Despite the initial appearance of NST under-utilization in tumors measuring between 3-5 cm, appropriate exclusion of patients not suitable for breast conservation and patient choice for mastectomy both emerged as leading factors for the omission of NST in this group. Use of NST is an important quality metric in optimizing breast conservation. Patient education and greater understanding of patient-related barriers to NST may help improve BCR.
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Affiliation(s)
- Ted James
- Department of Surgery, University of Vermont, Burlington, VT 05401, USA.
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Malkki M, Single R, Carrington M, Thomson G, Petersdorf E. MHC microsatellite diversity and linkage disequilibrium among common HLA-A, HLA-B, DRB1 haplotypes: implications for unrelated donor hematopoietic transplantation and disease association studies. ACTA ACUST UNITED AC 2005; 66:114-24. [PMID: 16029431 DOI: 10.1111/j.1399-0039.2005.00453.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Twenty-two human major histocompatibility complex (MHC) region microsatellite (Msat) markers were studied for diversity and linkage disequilibrium (LD) with HLA loci in hematopoietic cell transplant recipients and their HLA-A, HLA-B, HLA-C, HLA-DRB1, and HLA-DQB1 allele-matched unrelated donors. These Msats showed highly significant LD over much of the MHC region. The Msat diversity of five common Caucasian haplotypes (HLA-A1-B8-DR3, A3-B7-DR15, A2-B44-DR4, A29-B44-DR7, and A2-B7-DR15) was examined using a new measure called 'haplotype specific heterozygosity' (HSH). Each of the five haplotypes had at least one Msat marker with an HSH value of zero indicating that only one Msat allele was observed for the particular HLA haplotype. In addition, the ability of Msats to predict HLA-A-B-DRB1 haplotypes was studied. Over 90% prediction probability of two common haplotypes (HLA-A1-B8-DR3 and HLA-A3-B7-DR15) was achieved with information from three Msats (D6S265/D6S2787/D6S2894 and D6S510/D6S2810/D6S2876, respectively). We demonstrate how the HSH index can be used in the selection of informative Msats for transplantation and disease association studies. Markers with low HSH values can be used to predict specific HLA haplotypes or multilocus genotypes to supplement the screening of HLA-matched donors for transplantation. Markers with high HSH values will be most informative in studies investigating MHC region disease-susceptibility genes where HLA haplotypic effects are known to exist.
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Affiliation(s)
- M Malkki
- The Division of Clinical Research, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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Cook AD, Single R, McCahill LE. Surgical resection of primary tumors in patients who present with stage IV colorectal cancer: an analysis of surveillance, epidemiology, and end results data, 1988 to 2000. Ann Surg Oncol 2005; 12:637-45. [PMID: 15965730 DOI: 10.1245/aso.2005.06.012] [Citation(s) in RCA: 214] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2004] [Accepted: 03/08/2005] [Indexed: 12/17/2022]
Abstract
BACKGROUND Surgical resection of the primary tumor for patients who present with incurable stage IV colorectal cancer is controversial. National practice patterns have not been described. We evaluated the use of primary tumor resection in patients presenting with stage IV colorectal cancer. METHODS Patients with stage IV colorectal cancer diagnosed between 1988 and 2000 were selected from the Surveillance, Epidemiology, and End Results database. Patients undergoing primary tumor resection were analyzed on the basis of sex, race, year of diagnosis, and the anatomical site of the primary tumor. We compared the survival of resected and nonresected patients. RESULTS A total of 17,658 (66%) of the 26,754 patients presenting with stage IV colorectal cancer underwent primary tumor resection. Patients with resected disease were more likely to be young (mean age of 67.1 vs. 70.3 years) and to have right-sided tumors (75.3%, 73.0%, and 45.6%, respectively, for right, left, and rectal; P < .001). In all age groups, patients undergoing resection had higher median and 1-year survival rates (colon: 11 vs. 2 months, 45% vs. 12%, P < .001; rectum: 16 vs. 6 months, 59% vs. 25%, P < .001) when compared with patients who did not undergo resection. CONCLUSIONS Most patients who present with stage IV colorectal cancer undergo resection of the primary tumor. The proportion of patients undergoing resection depends on patient age and race and the anatomical location of the primary tumor. The degree to which case selection explains the treatment and survival differences observed is not known. Further investigation of the role of surgery in the management of incurable stage IV colorectal cancer is warranted.
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Affiliation(s)
- Alan D Cook
- Department of Surgery, Division of Surgerical Oncology, University of Vermont College of Medicine, Given Building, E-309, Burlington, Vermont 05405, USA
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Abstract
No proper statistical test is available for the evaluation of deviation of a single homozygous genotype from Hardy-Weinberg equilibrium (HWE) proportion. We propose a 1-d.f. chi2-test. The power of the proposed test is favorable compared to existing HWE testing procedures. The applications of this test are discussed.
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Affiliation(s)
- John J Chen
- Department of Preventive Medicine, State University of New York, Stony Brook, New York 11794, USA.
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Cao K, Moormann AM, Lyke KE, Masaberg C, Sumba OP, Doumbo OK, Koech D, Lancaster A, Nelson M, Meyer D, Single R, Hartzman RJ, Plowe CV, Kazura J, Mann DL, Sztein MB, Thomson G, Fernández-Viña MA. Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. ACTA ACUST UNITED AC 2004; 63:293-325. [PMID: 15009803 DOI: 10.1111/j.0001-2815.2004.00192.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The allelic and haplotypic diversity of the HLA-A, HLA-B, and HLA-C loci was investigated in 852 subjects from five sub-Saharan populations from Kenya (Nandi and Luo), Mali (Dogon), Uganda, and Zambia. Distributions of genotypes at all loci and in all populations fit Hardy-Weinberg equilibrium expectations. There was not a single allele predominant at any of the loci in these populations, with the exception of A*3002 [allele frequency (AF) = 0.233] in Zambians and Cw*1601 (AF = 0.283) in Malians. This distribution was consistent with balancing selection for all class I loci in all populations, which was evidenced by the homozygosity F statistic that was less than that expected under neutrality. Only in the A locus in Zambians and the C locus in Malians, the AF distribution was very close to neutrality expectations. There were six instances in which there were significant deviations of allele distributions from neutrality in the direction of balancing selection. All allelic lineages from each of the class I loci were found in all the African populations. Several alleles of these loci have intermediate frequencies (AF = 0.020-0.150) and seem to appear only in the African populations. Most of these alleles are widely distributed in the African continent and their origin may predate the separation of linguistic groups. In contrast to native American and other populations, the African populations do not seem to show extensive allelic diversification within lineages, with the exception of the groups of alleles A*02, A*30, B*57, and B*58. The alleles of human leukocyte antigen (HLA)-B are in strong linkage disequilibrium (LD) with alleles of the C locus, and the sets of B/C haplotypes are found in several populations. The associations between A alleles with C-blocks are weaker, and only a few A/B/C haplotypes (A*0201-B*4501-Cw*1601; A*2301-B*1503-Cw*0202; A*7401-B* 1503-Cw*0202; A*2902-B*4201-Cw*1701; A*3001-B*4201-Cw*1701; and A*3601-B*5301-Cw*0401) are found in multiple populations with intermediate frequencies [haplotype frequency (HF) = 0.010-0.100]. The strength of the LD associations between alleles of HLA-A and HLA-B loci and those of HLA-B and HLA-C loci was on average of the same or higher magnitude as those observed in other non-African populations for the same pairs of loci. Comparison of the genetic distances measured by the distribution of alleles at the HLA class I loci in the sub-Saharan populations included in this and other studies indicate that the Luo population from western Kenya has the closest distance with virtually all sub-Saharan population so far studied for HLA-A, a finding consistent with the putative origin of modern humans in East Africa. In all African populations, the genetic distances between each other are greater than those observed between European populations. The remarkable current allelic and haplotypic diversity in the HLA system as well as their variable distribution in different sub-Saharan populations is probably the result of evolutionary forces and environments that have acted on each individual population or in their ancestors. In this regard, the genetic diversity of the HLA system in African populations poses practical challenges for the design of T-cell vaccines and for the transplantation medical community to find HLA-matched unrelated donors for patients in need of an allogeneic transplant.
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Affiliation(s)
- K Cao
- Department of Oncology, Georgetown University, Washington, DC, USA
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Nicklas JA, Brooks EM, Hunter TC, Single R, Branda RF. Development of a quantitative PCR (TaqMan) assay for relative mitochondrial DNA copy number and the common mitochondrial DNA deletion in the rat. Environ Mol Mutagen 2004; 44:313-320. [PMID: 15476199 DOI: 10.1002/em.20050] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Changes in mitochondrial DNA copy number and increases in mitochondrial DNA mutations, especially deletions, have been associated with exposure to mutagens and with aging. Common deletions that are the result of recombination between direct repeats in human and rat (4,977 and 4,834, bp, respectively) are known to increase in tissues of aged individuals. Previous studies have used long-distance PCR and Southern blot or quantitative PCR to determine the frequency of deleted mitochondrial DNA. A quantitative PCR (TaqMan) assay was developed to detect both mitochondrial DNA copy number and deletion frequency in the rat. This methodology allows not only the determination of changes in the amount of mitochondrial DNA deletion relative to total mitochondrial DNA but also to determine changes in total mitochondrial DNA relative to genomic DNA. As a validation of the assay in rat liver, the frequency of the common 4,834 bp deletion is shown to increase with age, while the relative mitochondrial DNA copy number rises at a young age (3-60 days), then decreases and holds fairly steady to 2 years of age.
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Affiliation(s)
- Janice A Nicklas
- Genetics Laboratory and Vermont Cancer Center, University of Vermont, Burlington, Vermont 05401, USA
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