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Lee GKC, Barbosa C, Andersen G, Ramirez CJ, Kornya M, Abrams-Ogg A, Morrison K, Diamantino G, Wood RD, Beeler-Marfisi J, Ampuero F, Tatiersky L, Bienzle D. Cyclic hematopoiesis in a mixed-breed dog: case report and brief review. J Vet Diagn Invest 2022; 34:1006-1009. [PMID: 35904319 DOI: 10.1177/10406387221115179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
An 8-wk-old, male, mixed-breed puppy was adopted from a rescue organization. From the time of adoption, the puppy suffered episodes of illness affecting various organ systems, which resolved with supportive therapy but relapsed once medical therapy was discontinued. Review of the hematologic data revealed cyclic fluctuations in circulating blood cells. Cyclicity was most prominent in neutrophils, with recurrent severe neutropenia. Neutropenic episodes lasted 5-6 d, with regular cycles of 11-14 d between nadir neutrophil counts. Genetic testing determined that the patient was homozygous mutant for the frameshift mutation in the adaptor protein complex 3 β-subunit (AP3B1) gene, originally identified in gray collies with cyclic hematopoiesis (CH). Pedigree information was not available, but the patient's features were phenotypically distinct from those of collies. We describe here a case of the AP3B1 mutation in a mixed-breed dog that did not resemble a collie, undescribed previously, to our knowledge. Our findings indicate that the AP3B1 mutation and CH are present within the general canine population and are not restricted to collies.
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Affiliation(s)
- Gary K C Lee
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada.,Current address: Idexx Laboratories, Rydalmere, NSW, Australia
| | | | | | | | - Matthew Kornya
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | | | | | - R Darren Wood
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | - Fernanda Ampuero
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | | | - Dorothee Bienzle
- Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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Ballif BC, Emerson LJ, Ramirez CJ, Carl CR, Sundin K, Flores-Smith H, Shaffer LG. The PMEL gene and merle (dapple) in the dachshund: cryptic, hidden, and mosaic variants demonstrate the need for genetic testing prior to breeding. Hum Genet 2021; 140:1581-1591. [PMID: 34370083 DOI: 10.1007/s00439-021-02330-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/28/2021] [Accepted: 07/31/2021] [Indexed: 11/26/2022]
Abstract
One of the most unique coat color patterns in the domestic dog is merle (also known as dapple in the dachshund breed), characterized by patches of normal pigmentation surrounded by diluted eumelanin pigment. In dogs, this striking variegated pattern is caused by an insertion of a SINE element into the PMEL gene. Differences in the length of the SINE insertion [due to a variable-length poly(A)-tail] has been associated with variation in the merle coat color and patterning. We previously performed a systematic evaluation of merle in 175 Australian shepherds and related breeds and correlated the length of the merle insertion variants with four broad phenotypic clusters designated as "cryptic", "atypical", "classic", and "harlequin" merle. In this study, we evaluated the SINE insertions in 140 dachshunds and identified the same major merle phenotypic clusters with only slight variation between breeds. Specifically, we identified numerous cases of true "hidden" merle in dachshunds with light/red (pheomelanin) coats with little to no black/brown pigment (eumelanin) and thus minimal or no observable merle phenotype. In addition, we identified somatic and gonadal mosaicism, with one dog having a large insertion in the harlequin size range of M281 that had no merle phenotype and unintentionally produced a double merle puppy with anophthalmia. The frequent identification of cryptic, hidden, and mosaic merle variants, which can be undetectable by phenotypic inspection, should be of particular concern to breeders and illustrates the critical need for genetic testing for merle prior to breeding to avoid producing dogs with serious health problems.
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Affiliation(s)
- Blake C Ballif
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA.
| | | | - Christina J Ramirez
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Casey R Carl
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Kyle Sundin
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Helen Flores-Smith
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA, USA
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Shaffer LG, Geretschlaeger A, Ramirez CJ, Ballif BC, Carl C. Quality assurance checklist and additional considerations for canine clinical genetic testing laboratories: a follow-up to the published standards and guidelines. Hum Genet 2019; 138:501-508. [PMID: 30982136 PMCID: PMC6536464 DOI: 10.1007/s00439-019-02013-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/08/2019] [Indexed: 12/11/2022]
Abstract
There is currently no oversight for canine clinical genetic testing laboratories. We published an initial set of standards and guidelines with the goal of providing a basis for which canine testing laboratories could evaluate their quality assurance programs. To further those standards and guidelines, we have developed a checklist that can be used as a self-evaluation to identify gaps in their programs for continual quality improvement over time. Because there is currently no organization willing to oversee an external proficiency program, the checklist provides the first step toward an internal, self-assessment that can be used periodically to monitor improvements. In addition, we attempt to address concerns from the canine community regarding rare or private mutations, genetic screening using array-based technologies, non-peer reviewed tests that are being offered, and the clinical validity of certain mutations in particular breeds. Through coordination, conversation and hard work, the canine genetic testing community can strive to organize to improve testing and to provide more transparency to consumers and better outcomes for dogs.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA.
| | | | - Christina J Ramirez
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Blake C Ballif
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
| | - Casey Carl
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., 220 E Rowan, Suite 220, Spokane, WA, 99207, USA
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Ramirez CJ, Krug M, Zahand A, Sundin K, Shaffer LG, Ballif BC. Canine factor VII deficiency: lessons learned in applying methods-based laboratory proficiency testing. J Vet Diagn Invest 2019; 31:276-279. [PMID: 30661469 DOI: 10.1177/1040638718825281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Canine inherited factor VII deficiency is a mild-to-moderate, inherited coagulopathy that affects several breeds of dog. We identified 2 polymorphisms near the disease-causing F7 gene mutation, one of which interfered with testing in several Beagles by causing allele dropout of the normal, wild-type allele. In the absence of an external proficiency program among veterinary genetic testing laboratories, implementation of an internal proficiency program, which requires 2 independent methods for genotyping dogs at any given locus, was further enhanced by ensuring minimally non-overlapping primer pairs between the 2 assays. After redesign of our clinical tests, all dogs were re-examined, and the correct genotypes were identified. These changes ensure higher accuracy in future testing of the F7 mutation.
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Affiliation(s)
| | - Melissa Krug
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Adam Zahand
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Kyle Sundin
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Lisa G Shaffer
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
| | - Blake C Ballif
- Genetic Veterinary Sciences Inc., Paw Print Genetics, Spokane, WA
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Ballif BC, Ramirez CJ, Carl CR, Sundin K, Krug M, Zahand A, Shaffer LG, Flores-Smith H. The PMEL Gene and Merle in the Domestic Dog: A Continuum of Insertion Lengths Leads to a Spectrum of Coat Color Variations in Australian Shepherds and Related Breeds. Cytogenet Genome Res 2018; 156:22-34. [PMID: 30071510 DOI: 10.1159/000491408] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2018] [Indexed: 11/19/2022] Open
Abstract
Merle is a distinct coat color and pattern found in numerous species, including the domestic dog, characterized by patches of diluted eumelanin (black pigment) interspersed among areas of normal pigmentation. In dogs, this variegated pattern is caused by an insertion of a SINE element into the canine PMEL gene. Although variation in the length of the SINE insertion - due to a variable-length poly(A) tail - has been observed to be associated with variation in merle coat color and patterning, no systematic evaluation of this correlation has been conducted and published in the scientific literature. We performed high-resolution analysis of the SINE insertion lengths in 175 dogs (99 Australian shepherds, 45 miniature Australian shepherds, and 31 miniature American shepherds) and compared the genotypes with the coat phenotypes (when available). SINE insertion lengths varied from 201 to 277 bp, indicating that merle insertion variants can occur in virtually any size along the entire continuum. Genotype-phenotype correlation of 126 dogs with only a single SINE insertion (m/M) identified at least 4 major phenotypic clusters designated as "cryptic," "atypical," "classic," and "harlequin" merle. However, we found several phenotypic outliers that did not cluster within these major groupings, suggesting that insertion size is not the only factor responsible for merle phenotypic variability. In addition, we detected 25 dogs with 2 SINE insertions (M/M) and 24 dogs with more than 2 PMEL (merle) alleles, indicating mosaicism. Genotype-phenotype correlation of M/M dogs suggests that cryptic merle alleles often act like non-merle (m) alleles when combined with atypical, classic, and harlequin-sized alleles. The finding of mosaicism has important implications for the dog's phenotype and the ability to potentially transmit various alleles to its offspring. Furthermore, we identified examples of the SINE insertion poly(A)-tail expansion and contraction between generations, which also has important implications for breeding practices and determining mating pairs to avoid producing double merle dogs. These data demonstrate that there is a continuum of merle insertion lengths associated with a spectrum of coat color and patterns and that genotype-phenotype exceptions and overlap make it difficult to strictly assign certain insertion sizes with an expected coat color, although some generalizations are possible.
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Shaffer LG, Ramirez CJ, Phelps P, Aviram M, Walczak M, Bar-Gal GK, Ballif BC. An International Genetic Survey of Breed-Specific Diseases in Working Dogs from the United States, Israel, and Poland. Cytogenet Genome Res 2018; 153:198-204. [PMID: 29421799 DOI: 10.1159/000486774] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2017] [Indexed: 11/19/2022] Open
Abstract
Genetic diseases occur in breeds used for law enforcement. As important team members, dogs are expected to operate at peak performance for several years and are significant investments for both the initial purchase and extensive, specialized training. Previous studies have not focused on causes for retirement or euthanasia as genetic (inherited) versus acquired (environmental). We performed direct mutational analysis for breed-specific conditions on samples from 304 dogs including 267 law enforcement (122 US, 87 Israeli, and 58 Polish) and 37 search and rescue dogs. Genetic testing identified 29% (n = 89) of the dogs tested to be carriers of a genetic mutation and 6% (n = 19) to be at risk for a debilitating inherited condition that may eventually impair the dog's ability to work. At-risk dogs included Labrador Retrievers (n = 4) with exercise-induced collapse, Bloodhounds (n = 2) with degenerative myelopathy (DM), and German Shepherd dogs with DM (n = 12) or leukocyte adhesion deficiency, type III (n = 1). A substantial number of working dogs were shown to be at risk for genetic conditions that may shorten the dog's career. The loss of dogs, due to early retirement or euthanasia, as a result of preventable genetic conditions has an emotional cost to handlers and financial cost to service organizations that can be avoided with genetic screening prior to breeding, buying, or training.
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Affiliation(s)
- Lisa G Shaffer
- Paw Print Genetics, Genetic Veterinary Sciences, Inc., Spokane, WA, USA
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Shaffer LG, Ramirez CJ, Sundin K, Connell LB, Ballif BC. Genetic screening and mutation identification in a rare canine breed, the ceský fousek. Vet rec case rep 2017. [DOI: 10.1136/vetreccr-2016-000346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
- School of Molecular BiosciencesCollege of Veterinary MedicineWashington State UniversityPullmanWashingtonUSA
| | | | - Kyle Sundin
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
| | - Laurie B Connell
- Department of Molecular and Biomedical SciencesSchool of Marine SciencesUniversity of MaineOronoMaineUSA
| | - Blake C Ballif
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWashingtonUSA
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Spoor MS, Ramirez CJ, Daniel RJ, Shaw DP, Wininger FA, Whitney MS. What is your diagnosis? Pituitary mass in a dog. Vet Clin Pathol 2016; 45:381-2. [PMID: 27163433 DOI: 10.1111/vcp.12355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Melanie S Spoor
- Veterinary Medical Diagnostic Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine, Columbia, MO, USA
| | - Christina J Ramirez
- Veterinary Medical Diagnostic Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine, Columbia, MO, USA
| | - Rob J Daniel
- Veterinary Medical Teaching Hospital, Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Columbia, MO, USA
| | - Dan P Shaw
- Veterinary Medical Diagnostic Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine, Columbia, MO, USA
| | - Fred A Wininger
- Veterinary Medical Teaching Hospital, Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Columbia, MO, USA
| | - Marlyn S Whitney
- Veterinary Medical Diagnostic Laboratory, Department of Veterinary Pathobiology, College of Veterinary Medicine, Columbia, MO, USA
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Shaffer LG, Ramirez CJ, Sundin K, Carl C, Ballif BC. Genetic screening and mutation identification in a rare canine breed, the Drentsche patrijshond. Vet rec case rep 2015. [DOI: 10.1136/vetreccr-2015-000185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Lisa G Shaffer
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
- School of Molecular BiosciencesCollege of Veterinary MedicineWashington State UniversityPullmanWA99164USA
| | | | - Kyle Sundin
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
| | - Casey Carl
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
| | - Blake C Ballif
- Paw Print GeneticsGenetic Veterinary Sciences, IncSpokaneWAUSA
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Abstract
Six 12- to 14-month-old New Zealand White rabbits were diagnosed with copper toxicosis. These rabbits were part of a group of 110 purchased and shipped overnight for research purposes. On arrival, the group experienced an abrupt diet change. Eight died over 3 weeks and 6 were submitted for postmortem examination. Microscopic findings included severe centrilobular to midzonal hepatocellular necrosis with rhodanine stain-positive copper granules in the remaining hepatocytes. Mild periportal fibrosis and biliary hyperplasia, hemoglobinuric nephrosis, and splenic erythrophagocytosis were also observed. Hepatic copper concentrations were elevated, ranging from 319 to 997 ppm. Clinical disease was not previously observed in younger rabbits gradually transitioned from the supplier's copper-supplemented diet. Copper toxicosis likely occurred in these rabbits from a combination of (1) increased duration of copper supplementation leading to increased hepatocellular stores and (2) stress leading to anorexia and release of hepatocellular copper stores similar to chronic copper toxicosis as described in sheep.
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Affiliation(s)
- C J Ramirez
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 1600 E. Rollins St, Columbia, MO 65211, USA.
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Affiliation(s)
- Jane Ashley Stuckey
- Veterinary Medical Teaching Hospital, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
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Ramirez CJ, Fleming MA, Potter JD, Ostrander GK, Ostrander EA. Marsupial BRCA1: conserved regions in mammals and the potential effect of missense changes. Oncogene 2004; 23:1780-8. [PMID: 15001988 DOI: 10.1038/sj.onc.1207292] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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: 11/09/2022]
Abstract
More than half of the reported missense changes in the breast cancer susceptibility protein BRCA1 occur in exon 11, but none has been clearly identified as disease associated and only 28 are designated 'probable' neutral polymorphisms. Previously, in a comparison of sequences from 57 eutherian mammal species, we found seven 'highly conserved regions' between amino acids 282 and 1103, and identified 38 missense changes as likely to disrupt gene function. These conserved regions were also present in birds and amphibians and included only six of the mutations predicted to affect function. In this new analysis, we hypothesized that using 37 ancestral sequences derived from the 57 GenBank sequences and including eight marsupial sequences would allow us to identify regions unique to mammals and refine our predictions of disease-associated missense changes. We identified 13 conserved regions, three of which appear to be unique to mammals, and 21 likely disease-associated missense changes, 11 of which occur in conserved regions. Seven regions identified in this analysis, including the three found only in mammalian sequences, and nine missense changes predicted to affect function are in the putative STAT1-interaction domain, suggesting that the role of STAT1 in immune response is important to mammary function. The reduction in the number of missense changes predicted to be disease associated and the identification of conserved regions specific to mammals can facilitate the further study of the role of missense changes in BRCA1-associated breast cancers.
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Affiliation(s)
- Christina J Ramirez
- Divisions of Clinical Research and Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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Fleming MA, Potter JD, Ramirez CJ, Ostrander GK, Ostrander EA. Understanding missense mutations in the BRCA1 gene: an evolutionary approach. Proc Natl Acad Sci U S A 2003; 100:1151-6. [PMID: 12531920 PMCID: PMC298742 DOI: 10.1073/pnas.0237285100] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.0] [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] [Indexed: 11/18/2022] Open
Abstract
The role of missense changes in BRCA1 in breast cancer susceptibility has been difficult to establish. We used comparative evolutionary methods to identify potential functionally important amino acid sites in exon 11 and missense changes likely to disrupt gene function, aligning sequences from 57 eutherian mammals and categorizing amino acid sites by degree of conservation. We used Bayesian phylogenetic analyses to determine relationships among orthologs and identify codons evolving under positive selection. Most conserved residues occur in a region with the highest concentration of protein-interacting domains. Rapidly evolving residues are concentrated in the RAD51-interacting domain, suggesting that selection is acting most strongly on the role of BRCA1 in DNA repair. Investigation of the functional role of missense changes in breast-cancer susceptibility should focus on 38 missense changes in conserved and 3 in rapidly evolving regions of exon 11.
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Affiliation(s)
- Melissa A Fleming
- Divisions of Clinical Research and Human Biology, and Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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