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1.
Hum Mol Genet ; 27(14): 2454-2465, 2018 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-29726930

RESUMO

The 17 genes of the T-box family are transcriptional regulators that are involved in all stages of embryonic development, including craniofacial, brain, heart, skeleton and immune system. Malformation syndromes have been linked to many of the T-box genes. For example, haploinsufficiency of TBX1 is responsible for many structural malformations in DiGeorge syndrome caused by a chromosome 22q11.2 deletion. We report four individuals with an overlapping spectrum of craniofacial dysmorphisms, cardiac anomalies, skeletal malformations, immune deficiency, endocrine abnormalities and developmental impairments, reminiscent of DiGeorge syndrome, who are heterozygotes for TBX2 variants. The p.R20Q variant is shared by three affected family members in an autosomal dominant manner; the fourth unrelated individual has a de novo p.R305H mutation. Bioinformatics analyses indicate that these variants are rare and predict them to be damaging. In vitro transcriptional assays in cultured cells show that both variants result in reduced transcriptional repressor activity of TBX2. We also show that the variants result in reduced protein levels of TBX2. Heterologous over-expression studies in Drosophila demonstrate that both p.R20Q and p.R305H function as partial loss-of-function alleles. Hence, these and other data suggest that TBX2 is a novel candidate gene for a new multisystem malformation disorder.

2.
J Mol Diagn ; 16(5): 541-549, 2014 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-25017478

RESUMO

Next-generation sequencing shows great promise by allowing rapid mutational analysis of multiple genes in human cancers. Recently, we implemented the multiplex PCR-based Ion AmpliSeq Cancer Hotspot Panel (>200 amplicons in 50 genes) to evaluate EGFR, KRAS, and BRAF in lung and colorectal adenocarcinomas. In 10% of samples, automated analysis identified a novel G873R substitution mutation in EGFR. By examining reads individually, we found this mutation in >5% of reads in 50 of 291 samples and also found similar events in 18 additional amplicons. These apparent mutations are present only in short reads and within 10 bases of either end of the read. We therefore hypothesized that these were from panel primers promiscuously binding to nearly complementary sequences of nontargeted amplicons. Sequences around the mutations matched primer binding sites in the panel in 18 of 19 cases, thus likely corresponding to panel primers. Furthermore, because most primers did not show this effect, we demonstrated that next-generation sequencing may be used to better design multiplex PCR primers through iterative elimination of offending primers to minimize mispriming. Our results indicate the need for careful sequence analysis to avoid false-positive mutations that can arise in multiplex PCR panels. The AmpliSeq Cancer panel is a valuable tool for clinical diagnostics, provided awareness of potential artifacts.


Assuntos
Sequenciamento de Nucleotídeos em Larga Escala/métodos , Sequenciamento de Nucleotídeos em Larga Escala/normas , Reação em Cadeia da Polimerase Multiplex/métodos , Reação em Cadeia da Polimerase Multiplex/normas , Algoritmos , Biologia Computacional/métodos , Receptores ErbB/genética , Éxons , Humanos , Mutação , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
3.
Clin Lab Med ; 31(4): 543-64, viii, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22118736

RESUMO

Several new microdeletion and microduplication syndromes have been discovered in a genotype-first approach. Many of these disorders are caused by nonallelic homologous recombination between blocks of segmental duplication. The authors describe 9 regions for which copy number alteration is proposed to cause an abnormal phenotype. Some of these disorders have been observed in affected individuals and individuals lacking a clearly abnormal phenotype. These deletions and duplications are thought to be contributory, but not always sufficient, to elicit an abnormal outcome. Additional studies are necessary to further evaluate the penetrance and delineate the clinical spectrum associated with many of these newly described disorders.


Assuntos
Aberrações Cromossômicas , Transtornos Cromossômicos , Deleção de Genes , Duplicação Gênica , Análise de Sequência com Séries de Oligonucleotídeos , Análise Citogenética , Humanos , Síndrome
4.
Birth Defects Res A Clin Mol Teratol ; 82(10): 662-9, 2008 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-18937341

RESUMO

BACKGROUND: Neural tube defects (NTDs), including spina bifida and anencephaly, are the second most common birth defect with an incidence of 1/1000. Genetic factors are believed to contribute to NTD risk and family-based studies can be useful for identifying such risk factors. METHODS: We ascertained 1066 NTD families (1467 affected patients), including 307 multiplex NTD families. We performed pedigree analysis to describe the inheritance patterns, pregnancy outcomes, and recurrence risks to relatives of various types. RESULTS: Myelomeningocele or spina bifida (66.9%) and cranial defects (17.7%) were the most common NTD subtypes observed. The overall male:female ratio for affected individuals was 0.82, and there were even fewer males among individuals with an upper level NTD (0.62). Among twins, 2 of the 5 monozygotic twins and only 3 of 35 dizygotic twins were concordant, while 27% of the same sex twins were concordant, but none of the different sex twins. The estimated 6.3% recurrence risk to siblings (CI 0.04-0.08) is consistent with previous reports. Families with two or more affected individuals show a higher proportion of female transmitters (p = 0.0002). Additionally, the number of affected relatives in maternal compared to paternal lineages was more than double (p = 0.006). There were significantly more miscarriages, infant deaths, and stillborn pregnancies of the maternal aunts and uncles (p < 0.0001) and of first cousins (p = 0.04). CONCLUSIONS: Our data provide several lines of evidence consistent with a maternal effect, as well as a sex-influenced effect, in the etiology of NTDs.


Assuntos
Defeitos do Tubo Neural/genética , Família , Feminino , Humanos , Masculino , Mães , Defeitos do Tubo Neural/diagnóstico , Defeitos do Tubo Neural/epidemiologia , Linhagem , Gravidez , Resultado da Gravidez , Fatores de Risco , Fatores Sexuais , Gêmeos
5.
Environ Health Perspect ; 114(10): 1547-52, 2006 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-17035141

RESUMO

BACKGROUND: Folate metabolism pathway genes have been examined for association with neural tube defects (NTDs) because folic acid supplementation reduces the risk of this debilitating birth defect. Most studies addressed these genes individually, often with different populations providing conflicting results. OBJECTIVES: Our study evaluates several folate pathway genes for association with human NTDs, incorporating an environmental cofactor: maternal folate supplementation. METHODS: In 304 Caucasian American NTD families with myelomeningocele or anencephaly, we examined 28 polymorphisms in 11 genes: folate receptor 1, folate receptor 2, solute carrier family 19 member 1, transcobalamin II, methylenetetrahydrofolate dehydrogenase 1, serine hydroxymethyl-transferase 1, 5,10-methylenetetrahydrofolate reductase (MTHFR), 5-methyltetrahydrofolate-homo-cysteine methyltransferase, 5-methyltetrahydrofolate-homocysteine methyltransferase reductase, betaine-homocysteine methyltransferase (BHMT), and cystathionine-beta-synthase. RESULTS: Only single nucleotide polymorphisms (SNPs) in BHMT were significantly associated in the overall data set; this significance was strongest when mothers took folate-containing nutritional supplements before conception. The BHMT SNP rs3733890 was more significant when the data were stratified by preferential transmission of the MTHFR rs1801133 thermolabile T allele from parent to offspring. Other SNPs in folate pathway genes were marginally significant in some analyses when stratified by maternal supplementation, MTHFR, or BHMT allele transmission. CONCLUSIONS: BHMT rs3733890 is significantly associated in our data set, whereas MTHFR rs1801133 is not a major risk factor. Further investigation of folate and methionine cycle genes will require extensive SNP genotyping and/or resequencing to identify novel variants, inclusion of environmental factors, and investigation of gene-gene interactions in large data sets.


Assuntos
Ácido Fólico/metabolismo , Defeitos do Tubo Neural/genética , Alelos , Suplementos Nutricionais , Ácido Fólico/administração & dosagem , Humanos , Polimorfismo de Nucleotídeo Único
6.
Birth Defects Res A Clin Mol Teratol ; 73(11): 868-75, 2005 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-16237707

RESUMO

BACKGROUND: Vitamin A (retinol), in the form of retinoic acid (RA), is essential for normal development of the human embryo. Studies in the mouse and zebrafish have shown that retinol is metabolized in the developing spinal cord and must be maintained in a precise balance along the anteroposterior axis. Both excess and deficiency of RA can affect morphogenesis, including failures of neural tube closure. METHODS: We chose to investigate 5 genes involved in the metabolism or synthesis of RA, ALDH1A2, CYP26A1, CYP26B1, CRABP1, and CRABP2, for their role in the development of human neural tube defects, such as spina bifida. RESULTS: An association analysis using both allelic and genotypic single-locus tests revealed a significant association between the risk for spina bifida and 3 polymorphisms in the gene ALDH1A2; however, we found no evidence of a significant multilocus association. CONCLUSIONS: These results may suggest that polymorphisms in ALDH1A2 may influence the risk for lumbosacral myelomeningocele in humans.


Assuntos
Alelos , Meningomielocele/enzimologia , Oxirredutases/genética , Polimorfismo Genético , Receptores do Ácido Retinoico/genética , Animais , Análise Mutacional de DNA , Feminino , Predisposição Genética para Doença , Humanos , Desequilíbrio de Ligação , Masculino , Meningomielocele/genética , Meningomielocele/metabolismo , Camundongos , Organogênese/genética , Locos de Características Quantitativas , Vitamina A/genética , Vitamina A/metabolismo
7.
Hum Genet ; 117(2-3): 133-42, 2005 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-15883837

RESUMO

Neural tube defects (NTDs) are common birth defects, occurring in approximately 1/1,000 births; both genetic and environmental factors are implicated. To date, no major genetic risk factors have been identified. Throughout development, cell adhesion molecules are strongly implicated in cell-cell interactions, and may play a role in the formation and closure of the neural tube. To evaluate the role of neural cell adhesion molecule 1 (NCAM1) in risk of human NTDs, we screened for novel single-nucleotide polymorphisms (SNPs) within the gene. Eleven SNPs across NCAM1 were genotyped using TaqMan. We utilized a family-based approach to evaluate evidence for association and/or linkage disequilibrium. We evaluated American Caucasian simplex lumbosacral myelomeningocele families (n=132 families) using the family based association test (FBAT) and the pedigree disequilibrium test (PDT). Association analysis revealed a significant association between risk for NTDs and intronic SNP rs2298526 using both the FBAT test (P=0.0018) and the PDT (P=0.0025). Using the HBAT version of the FBAT to look for haplotype association, all pairwise comparisons with SNP rs2298526 were also significant. A replication study set, consisting of 72 additional families showed no significant association; however, the overall trend for overtransmission of the less common allele of SNP rs2298526 remained significant in the combined sample set. In addition, we analyzed the expression pattern of the NCAM1 protein in human embryos, and while NCAM1 is not expressed within the neural tube at the time of closure, it is expressed in the surrounding and later in differentiated neurons of the CNS. These results suggest variations in NCAM1 may influence risk for human NTDs.


Assuntos
Íntrons/genética , Desequilíbrio de Ligação/genética , Meningocele/genética , Moléculas de Adesão de Célula Nervosa/genética , Polimorfismo de Nucleotídeo Único , Regulação da Expressão Gênica no Desenvolvimento/genética , Haplótipos/genética , Humanos , Meningocele/metabolismo , Meningocele/patologia , Moléculas de Adesão de Célula Nervosa/biossíntese , Linhagem , Medula Espinal/embriologia , Medula Espinal/patologia
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