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Tatarian J, Tupper N, Li P, Feusier J, Abdo M, Hyter S, Gonzales PR, Zhang D, Woodroof J, Kelting S, Godwin AK, Cui W. Morphologic, immunophenotypic, molecular genetic, and clinical characterization in patients with SRSF2-mutated acute myeloid leukemia. Am J Clin Pathol 2023; 160:490-499. [PMID: 37458189 PMCID: PMC10629464 DOI: 10.1093/ajcp/aqad077] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 09/21/2023] Open
Abstract
OBJECTIVES SRSF2 mutations are known to be associated with poor outcomes in myelodysplastic neoplasm, but studies on their prognostic impact on acute myeloid leukemia (AML) remain limited. In this retrospective study, we analyzed clinical and pathologic characteristics of patients with AML and correlated the outcomes with SRSF2 mutations. METHODS We characterized the morphologic, immunophenotypic, molecular, and clinical findings in AML with mutated SRSF2 and compared them with SRSF2 wild-type (WT) myeloid neoplasms (MNs). RESULTS Using next-generation sequencing, we identified 134 patients with MNs and SRSF2 mutations (85 with AML and 49 with MNs) in addition to 342 SRSF2-WT AMLs. Fifty-two (62%) patients with altered SRSF2 demonstrated a variable degree of morphologic dysplasia. The most frequent immunophenotypic aberrancies in SRSF2-mutant AML included diminished CD33 expression and overexpression of CD7, CD56, or CD123, similar to WT AML. More IDH1/2 (P = .015) and NPM1 (P = .002) mutations were seen in SRSF2-mutant AML than in SRSF2-mutant non-AML. Further, more IDH1/2, ASXL1, RUNX1, and STAG2 mutations were observed in SRSF2-mutant AML than in SRSF2-WT AML (P < .0001 to P = .001). Finally, patients with SRSF2-mutant AML showed a significantly worse overall survival (OS) than patients with SRSF2-WT AML (P < .0001), but this worse OS appeared to be rescued by allogeneic stem cell transplant (allo-SCT). CONCLUSIONS Acute myeloid leukemia with altered SRSF2 shows a variable degree of morphologic dysplasia without uniform immunophenotypic aberrancies. SRSF2 mutations appear to be independent poor prognostic factors, but allo-SCT has improved the clinical outcomes in patients with SRSF2-mutant AML.
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Affiliation(s)
- Joshua Tatarian
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Natalie Tupper
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Peng Li
- Division of Hematopathology, Department of Pathology, University of Utah, Salt Lake City, UT, US
| | - Julie Feusier
- Division of Hematopathology, Department of Pathology, University of Utah, Salt Lake City, UT, US
| | - Maryam Abdo
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Stephen Hyter
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Patrick R Gonzales
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Da Zhang
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Janet Woodroof
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Sarah Kelting
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Andrew K Godwin
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, KS, US
| | - Wei Cui
- Department of Pathology & Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, US
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Tayeh MK, Chen M, Fullerton SM, Gonzales PR, Huang SJ, Massingham LJ, O'Daniel JM, Stewart DR, Stiles AR, Evans BJ. The designated record set for clinical genetic and genomic testing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100342. [PMID: 36547466 DOI: 10.1016/j.gim.2022.11.010] [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] [Received: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Margaret Chen
- Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI; GeneDx, Gaithersburg, MD
| | - Stephanie M Fullerton
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA
| | - Patrick R Gonzales
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Lenexa, KS
| | - Samuel J Huang
- Division of Medical Genetics, Marshfield Clinic, Marshfield, WI
| | - Lauren J Massingham
- Division of Medical Genetics, Department of Pediatrics, Hasbro Children's Hospital, Providence, RI; The Warren Alpert School of Medicine at Brown University, Providence, RI
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Ashlee R Stiles
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Barbara J Evans
- Levin College of Law, University of Florida, Gainesville, FL; Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL
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- American College of Medical Genetics and Genomics, Bethesda, MD
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Gonzales PR, Andersen EF, Brown TR, Horner VL, Horwitz J, Rehder CW, Rudy NL, Robin NH, Thorland EC, On Behalf Of The Acmg Laboratory Quality Assurance Committee. Interpretation and reporting of large regions of homozygosity and suspected consanguinity/uniparental disomy, 2021 revision: A technical standard of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:255-261. [PMID: 34906464 DOI: 10.1016/j.gim.2021.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/18/2022] Open
Abstract
Genomic testing, including single-nucleotide variation (formerly single-nucleotide polymorphism)-based chromosomal microarray and exome and genome sequencing, can detect long regions of homozygosity (ROH) within the genome. Genomic testing can also detect possible uniparental disomy (UPD). Platforms that can detect ROH and possible UPD have matured since the initial American College of Medical Genetics and Genomics (ACMG) standard was published in 2013, and the detection of ROH and UPD by these platforms has shown utility in diagnosis of patients with genetic/genomic disorders. The presence of these segments, when distributed across multiple chromosomes, may indicate a familial relationship between the proband's parents. This technical standard describes the detection of possible consanguinity and UPD by genomic testing, as well as the factors confounding the inference of a specific parental relationship or UPD. Current bioethical and legal issues regarding detection and reporting of consanguinity are also discussed.
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Affiliation(s)
| | - Erica F Andersen
- ARUP Laboratories, Salt Lake City, UT; The University of Utah, Salt Lake City, UT
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Upadia J, Gonzales PR, Atkinson TP, Schroeder HW, Robin NH, Rudy NL, Mikhail FM. A previously unrecognized 22q13.2 microdeletion syndrome that encompasses TCF20 and TNFRSF13C. Am J Med Genet A 2018; 176:2791-2797. [PMID: 30216695 DOI: 10.1002/ajmg.a.40492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 05/01/2018] [Accepted: 07/03/2018] [Indexed: 12/23/2022]
Abstract
Phelan-McDermid syndrome (PMS, OMIM 606232) is a heterozygous contiguous gene microdeletion syndrome occurring at the distal region of chromosome 22q13. This deletion encompasses the SHANK3 gene at 22q13.33, which is thought to be the critical gene for the neurodevelopmental features seen in this syndrome. PMS is typically characterized by intellectual disability, autism spectrum disorder, absent to severely delayed speech, neonatal hypotonia, and dysmorphic features. Two patients presenting with classic clinical features of PMS have been reported to have interstitial microdeletions in the 22q13.2 region that map proximal to the SHANK3 gene (0.54 and 0.72 Mb, respectively). Here, we describe a 13-month-old girl with a de novo 1.16 Mb interstitial deletion in the 22q13.2 region who presented with global developmental delay, subtle dysmorphic features, and immunodeficiency. This deletion overlaps with the two previously published cases and five cases from the DECIPHER database. All eight patients share features common to patients with PMS including developmental delay and language delay, which suggests that this represents a previously unrecognized microdeletion syndrome in the 22q13.2 region. Our patient's deletion encompasses the TCF20 and TNFRSF13C genes, which are thought to play causative roles in the patient's neurodevelopmental and immunological features, respectively.
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Affiliation(s)
- Jariya Upadia
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Patrick R Gonzales
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Harry W Schroeder
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Fady M Mikhail
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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Wang X, Kallionpää RA, Gonzales PR, Chitale DA, Tousignant RN, Crowley JP, Chen Z, Yoder SJ, Blakeley JO, Acosta MT, Korf BR, Messiaen LM, Tainsky MA. Germline and Somatic NF1 Alterations Are Linked to Increased HER2 Expression in Breast Cancer. Cancer Prev Res (Phila) 2018; 11:655-664. [PMID: 30104415 DOI: 10.1158/1940-6207.capr-18-0072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/21/2018] [Accepted: 08/07/2018] [Indexed: 02/06/2023]
Abstract
NF1 germline mutation predisposes to breast cancer. NF1 mutations have also been proposed as oncogenic drivers in sporadic breast cancers. To understand the genomic and histologic characteristics of these breast cancers, we analyzed the tumors with NF1 germline mutations and also examined the genomic and proteomic profiles of unselected tumors. Among 14 breast cancer specimens from 13 women affected with neurofibromatosis type 1 (NF1), 9 samples (NF + BrCa) underwent genomic copy number (CN) and targeted sequencing analysis. Mutations of NF1 were identified in two samples and TP53 were in three. No mutation was detected in ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, NBN, PALB2, PTEN, RAD50, and STK11 HER2 (ErbB2) overexpression was detected by IHC in 69.2% (9/13) of the tumors. CN gain/amplification of ERBB2 was detected in 4 of 9 with DNA analysis. By evaluating HER2 expression and NF1 alterations in unselected invasive breast cancers in TCGA datasets, we discovered that among samples with ERBB2 CN gain/amplification, the HER2 mRNA and protein expression were much more pronounced in NF1-mutated/deleted samples in comparison with NF1-unaltered samples. This finding suggests a synergistic interplay between these two genes, potentially driving the development of breast cancer harboring NF1 mutation and ERBB2 CN gain/amplification. NF1 gene loss of heterozygosity was observed in 4 of 9 NF + BrCa samples. CDK4 appeared to have more CN gain in NF + BrCa and exhibited increased mRNA expression in TCGA NF1--altered samples. Cancer Prev Res; 11(10); 655-64. ©2018 AACR.
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Affiliation(s)
- Xia Wang
- H Lee Moffitt Cancer Center and Research Institute, Tampa, Florida.
| | - Roope A Kallionpää
- Department of Dermatology and Venereology, Institute of Biomedicine, University of Turku, Turku, Finland
| | | | | | | | | | - Zhihua Chen
- H Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Sean J Yoder
- H Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | | | - Maria T Acosta
- Children's National Health System, George Washington University, Washington, DC
| | - Bruce R Korf
- The University of Alabama at Birmingham, Birmingham, Alabama
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Upadia J, Gonzales PR, Robin NH. Novel de novo pathogenic variant in the NR2F2 gene in a boy with congenital heart defect and dysmorphic features. Am J Med Genet A 2018; 176:1423-1426. [PMID: 29663647 DOI: 10.1002/ajmg.a.38700] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 03/04/2018] [Accepted: 03/12/2018] [Indexed: 11/06/2022]
Abstract
The NR2F2 gene plays an important role in angiogenesis and heart development. Moreover, this gene is involved in organogenesis in many other organs in mouse models. Variants in this gene have been reported in a number of patients with nonsyndromic atrioventricular septal defect, and in one patient with congenital heart defect and dysmorphic features. Here we report an 11-month-old Caucasian male with global developmental delay, dysmorphic features, coarctation of the aorta, and ventricular septal defect. He was later found to have a pathogenic mutation in the NR2F2 gene by whole exome sequencing. This is the second instance in which an NR2F2 mutation has been identified in a child with a congenital heart defect and other anomalies. This case suggests that some variants in NR2F2 may cause syndromic forms of congenital heart defect.
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Affiliation(s)
- Jariya Upadia
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Patrick R Gonzales
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nathaniel H Robin
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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Abstract
Chromosome analysis is one of the first approaches to genetic testing and remains a key component of genetic analysis of constitutional and somatic genetic disorders. Numerical or unbalanced structural chromosome abnormalities usually lead to multiple congenital anomalies. Sometimes these are compatible with live birth, usually resulting in severe cognitive and physical handicaps; other times they result in miscarriage or stillbirth. Chromosome rearrangements also occur as somatic changes in malignancies. Identification of constitutional chromosomal anomalies (anomalies present in most or all cells of the body and/or the germline) can provide important information for genetic counseling. In this unit, we introduce chromosomal microarray analysis (CMA), which is a relatively recent addition to cytogenetic technologies, and has become the recommended first-tier testing method for patients with developmental delay, intellectual disability, autism, and/or multiple congenital anomalies. We also discuss non-invasive prenatal testing/screening (NIPTS), which uses circulating cell-free fetal DNA (cfDNA) from maternal plasma to rapidly screen for autosomal and sex-chromosome aneuploidies. Cytogenetic analysis of tumors is helpful in diagnosis and in monitoring the effects of treatment. The protocols in this chapter cover the clinical study of chromosomes in nonmalignant tissues.
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Affiliation(s)
- Patrick R Gonzales
- Cytogenetics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Andrew J Carroll
- Cytogenetics Laboratory, Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
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Gonzales PR, Pesesky MW, Bouley R, Ballard A, Biddy BA, Suckow MA, Wolter WR, Schroeder VA, Burnham CAD, Mobashery S, Chang M, Dantas G. Synergistic, collaterally sensitive β-lactam combinations suppress resistance in MRSA. Nat Chem Biol 2015; 11:855-61. [PMID: 26368589 PMCID: PMC4618095 DOI: 10.1038/nchembio.1911] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most prevalent multidrug-resistant pathogens worldwide, exhibiting increasing resistance to the latest antibiotic therapies. Here we show that the triple β-lactam combination meropenem-piperacillin-tazobactam (ME/PI/TZ) acts synergistically and is bactericidal against MRSA subspecies N315 and 72 other clinical MRSA isolates in vitro and clears MRSA N315 infection in a mouse model. ME/PI/TZ suppresses evolution of resistance in MRSA via reciprocal collateral sensitivity of its constituents. We demonstrate that these activities also extend to other carbapenem-penicillin-β-lactamase inhibitor combinations. ME/PI/TZ circumvents the tight regulation of the mec and bla operons in MRSA, the basis for inducible resistance to β-lactam antibiotics. Furthermore, ME/PI/TZ subverts the function of penicillin-binding protein-2a (PBP2a) via allostery, which we propose as the mechanism for both synergy and collateral sensitivity. Showing in vivo activity similar to that of linezolid, ME/PI/TZ demonstrates that combinations of older β-lactam antibiotics could be effective against MRSA infections in humans.
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Affiliation(s)
- Patrick R. Gonzales
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Mitchell W. Pesesky
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Renee Bouley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Anna Ballard
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Brent A. Biddy
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Mark A. Suckow
- Freimann Life Sciences Center and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - William R. Wolter
- Freimann Life Sciences Center and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Valerie A. Schroeder
- Freimann Life Sciences Center and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Carey-Ann D. Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Shahriar Mobashery
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mayland Chang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Gautam Dantas
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, Missouri 63108, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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Alvarado DM, Aferol H, McCall K, Huang JB, Techy M, Buchan J, Cady J, Gonzales PR, Dobbs MB, Gurnett CA. Familial isolated clubfoot is associated with recurrent chromosome 17q23.1q23.2 microduplications containing TBX4. Am J Hum Genet 2010; 87:154-60. [PMID: 20598276 DOI: 10.1016/j.ajhg.2010.06.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 06/05/2010] [Accepted: 06/14/2010] [Indexed: 01/27/2023] Open
Abstract
Clubfoot is a common musculoskeletal birth defect for which few causative genes have been identified. To identify the genes responsible for isolated clubfoot, we screened for genomic copy-number variants with the Affymetrix Genome-wide Human SNP Array 6.0. A recurrent chromosome 17q23.1q23.2 microduplication was identified in 3 of 66 probands with familial isolated clubfoot. The chromosome 17q23.1q23.2 microduplication segregated with autosomal-dominant clubfoot in all three families but with reduced penetrance. Mild short stature was common and one female had developmental hip dysplasia. Subtle skeletal abnormalities consisted of broad and shortened metatarsals and calcanei, small distal tibial epiphyses, and thickened ischia. Several skeletal features were opposite to those described in the reciprocal chromosome 17q23.1q23.2 microdeletion syndrome associated with developmental delay and cardiac and limb abnormalities. Of note, during our study, we also identified a microdeletion at the locus in a sibling pair with isolated clubfoot. The chromosome 17q23.1q23.2 region contains the T-box transcription factor TBX4, a likely target of the bicoid-related transcription factor PITX1 previously implicated in clubfoot etiology. Our result suggests that this chromosome 17q23.1q23.2 microduplication is a relatively common cause of familial isolated clubfoot and provides strong evidence linking clubfoot etiology to abnormal early limb development.
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Gonzales PR, Walston TD, Camacho LO, Kielar DM, Church FC, Rezaie AR, Cooper ST. Mutation of the H-helix in antithrombin decreases heparin stimulation of protease inhibition. Biochim Biophys Acta 2007; 1774:1431-7. [PMID: 17905675 PMCID: PMC2215310 DOI: 10.1016/j.bbapap.2007.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2007] [Revised: 08/14/2007] [Accepted: 08/15/2007] [Indexed: 11/24/2022]
Abstract
Blood clotting proceeds through the sequential proteolytic activation of a series of serine proteases, culminating in thrombin cleaving fibrinogen into fibrin. The serine protease inhibitors (serpins) antithrombin (AT) and protein C inhibitor (PCI) both inhibit thrombin in a heparin-accelerated reaction. Heparin binds to the positively charged D-helix of AT and H-helix of PCI. The H-helix of AT is negatively charged, and it was mutated to contain neutral or positively charged residues to see if they contributed to heparin stimulation or protease specificity in AT. To assess the impact of the H-helix mutations on heparin stimulation in the absence of the known heparin-binding site, negative charges were also introduced in the D-helix of AT. AT with both positively charged H- and D-helices showed decreases in heparin stimulation of thrombin and factor Xa inhibition by 10- and 5-fold respectively, a decrease in affinity for heparin sepharose, and a shift in the heparin template curve. In the absence of a positively charged D-helix, changing the H-helix from neutral to positively charged increased heparin stimulation of thrombin inhibition 21-fold, increased heparin affinity and restored a normal maximal heparin concentration for inhibition.
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Affiliation(s)
- Patrick R Gonzales
- Biology Department, University of Wisconsin-La Crosse, La Crosse, WI 54601, USA
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Thorland EC, Gonzales PR, Gliem TJ, Wiktor AE, Ketterling RP. Comprehensive validation of array comparative genomic hybridization platforms: how much is enough? Genet Med 2007; 9:632-41. [PMID: 17873652 DOI: 10.1097/gim.0b013e31814629fc] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Clinical testing using various array comparative genomic hybridization platforms is being incorporated rapidly into cytogenetic testing algorithms. Comprehensive validation of these complex assays presents unique challenges and very few studies reporting the validation of commercially available array platforms have been published. Sixty-seven patients with previously defined subtelomere abnormalities, representing deletions and/or duplications of all 41 clinically relevant sites, were tested in a blinded study using the Spectral Genomics Constitutional Chip 3.0. Overall, 72 of 74 (97%) subtelomeric abnormalities were concordant with previous cytogenetic studies. However, two false-negative results were documented, and issues with mismapped and suboptimal clone performance were identified that may result in failure to detect 6q and 20q subtelomeric abnormalities. The results of this study indicate that comprehensive validation is necessary before implementation of array comparative genomic hybridization platforms into a clinical setting. Specific suggestions for validation are discussed in the context of the recently proposed American College of Medical Genetics guidelines for microarray analysis for constitutional cytogenetic abnormalities.
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Affiliation(s)
- Erik C Thorland
- Cytogenetics Laboratory, Division of Laboratory Genetics, Department of Laboratory Genetics and Pathology, Mayo Clinic, 200 First St. SW, Rochester, Minnesota, USA.
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Shearer BM, Thorland EC, Gonzales PR, Ketterling RP. Evaluation of a commercially available focused aCGH platform for the detection of constitutional chromosome anomalies. Am J Med Genet A 2007; 143A:2357-70. [PMID: 17853469 DOI: 10.1002/ajmg.a.31954] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microarray-based comparative genomic hybridization (aCGH) allows for simultaneous high-resolution analysis of multiple genomic loci. Recently, focused aCGH platforms have emerged allowing for analysis of numerous clinically relevant chromosome loci. The purpose of our study was to evaluate the Spectral Genomics Constitutional Chip 1.0 (CC) for use in the clinical laboratory. The CC consisted of 429 BAC clones for 41 known genetic deletion/duplication syndromes, subtelomeric regions, and chromosomal backbone clones. We conducted a blinded study of 48 samples including 46 patients (one sample was run in triplicate) with previously determined constitutional chromosome anomalies and two negative controls. Patient samples included 31 microdeletions, four duplications, three derivative chromosomes, three trisomies, and five sex chromosome aneuploidies. Our results show that the CC identified the expected gains and/or losses in 46 of 48 samples. The two negative controls were considered to be normal and the three replicates of the same patient sample were concordant. Two samples yielded false-negative results; however, repeat analysis produced acceptable results for one of them. One sample ultimately had an insufficient amount of DNA precluding aCGH analysis. While promising, the results suggest that further studies are needed to reduce protocol variability and to establish standard analysis and interpretation criteria. Further, this study verifies the importance of extensive validation studies prior to clinical implementation of new clinically available methodologies.
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Affiliation(s)
- Brandon M Shearer
- Division of Laboratory Genetics, Mayo Clinic, Rochester, Minnesota 55905, USA
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Klein RD, Thorland EC, Gonzales PR, Beck PA, Dykas DJ, McGrath JM, Bale AE. A multiplex assay for the detection and mapping of complex glycerol kinase deficiency. Clin Chem 2006; 52:1864-70. [PMID: 16887896 DOI: 10.1373/clinchem.2006.072397] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 11/06/2022]
Abstract
BACKGROUND Glycerol kinase deficiency (GKD) is an X-linked recessive disorder that presents in both isolated and complex forms. The contiguous deletion that leads to GKD also commonly affects NR0B1 (DAX1), the gene associated with adrenal hypoplasia congenita, and DMD, the Duchenne muscular dystrophy gene. Molecular testing to delineate this deletion is expensive and has only limited availability. METHODS We designed a multiplex PCR assay for the detection and mapping of a contiguous deletion potentially affecting the IL1RAPL1, NR0B1, GK, and DMD genes in a 29-month-old male patient with GKD. RESULTS Multiplex PCR detected a contiguous deletion that involved the IL1RAPL1, NR0B1, GK, and DMD genes. Although the patient had a creatine kinase concentration within the reference interval, further mapping with PCR revealed that exon 74 was the last intact exon at the 3' end of the DMD gene. CONCLUSIONS Multiplex PCR is an effective and inexpensive way to detect and map the contiguous deletion in cases of complex GKD. The extension of a deletion to include DMD exon 75 in a patient with a creatine kinase concentration within the reference interval suggests that this region of the gene may not be essential for protein function.
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Affiliation(s)
- Roger D Klein
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55901, USA.
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