RP-Department of Health Management & Informatics

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Browsing RP-Department of Health Management & Informatics by Author "Chiavacci, R. M."

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    AGC1 Deficiency Causes Infantile Epilepsy, Abnormal Myelination, and Reduced N-Acetylaspartate.
    (2014) Otieno, F. G.; Falk, M.J.; Li, D.; Gai, X.; McCormick, E.; Place, E.; Lasorsa, F.M.; Hou, C.; Kim, C.E.; Abdel-Magid, N.; Vazquez, L.; Mentch, F.D.; Chiavacci, R. M.; Liang, J.; Liu, X.; Jiang, H.; Giannuzzi, G.; Marsh, E.D.; Yiran, G.; Tian, L.; Palmieri, F.; Hakonarson, H.
    BACKGROUND: Whole exome sequencing (WES) offers a powerful diagnostic tool to rapidly and efficiently sequence all coding genes in individuals presenting for consideration of phenotypically and genetically heterogeneous disorders such as suspected mitochondrial disease. Here, we report results of WES and functional validation in a consanguineous Indian kindred where two siblings presented with profound developmental delay, congenital hypotonia, refractory epilepsy, abnormal myelination, fluctuating basal ganglia changes, cerebral atrophy, and reduced N-acetylaspartate (NAA). METHODS: Whole blood DNA from one affected and one unaffected sibling was captured by Agilent SureSelect Human All Exon kit and sequenced on the Illumina HiSeq2000. Mutations were validated by Sanger sequencing in all family members. Protein from wild-type and mutant fibroblasts was isolated to assess mutation effects on protein expression and enzyme activity. RESULTS: A novel SLC25A12 homozygous missense mutation, c.1058G>A; p.Arg353Gln, segregated with disease in this kindred. SLC25A12 encodes the neuronal aspartate-glutamate carrier 1 (AGC1) protein, an essential component of the neuronal malate/aspartate shuttle that transfers NADH and H(+) reducing equivalents from the cytosol to mitochondria. AGC1 activity enables neuronal export of aspartate, the glial substrate necessary for proper neuronal myelination. Recombinant mutant p.Arg353Gln AGC1 activity was reduced to 15% of wild type. One prior reported SLC25A12 mutation caused complete loss of AGC1 activity in a child with epilepsy, hypotonia, hypomyelination, and reduced brain NAA. CONCLUSIONS: These data strongly suggest that SLC25A12 disease impairs neuronal AGC1 activity. SLC25A12 sequencing should be considered in children with infantile epilepsy, congenital hypotonia, global delay, abnormal myelination, and reduced brain NAA.
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    Association analysis of the FTO gene with obesity in children of Caucasian and African ancestry reveals a common tagging SNP
    (Public Library of Science, 2008-03) Grant, S.F.; Li, M.; Bradfield, J.P.; Kim, C.E.; Annaiah, K.; Santa, E.; Glessner, J.T.; Casalunovo, T.; Frackelton, E.C.; Otieno, George Ochieng; Shaner, J.L.; Smith, R.M.; Imielinski, M.; Eckert, A. W.; Chiavacci, R. M.; Berkowitz, R.I.; Hakonarson, H.
    Recently an association was demonstrated between the single nucleotide polymorphism (SNP), rs9939609, within the FTO locus and obesity as a consequence of a genome wide association (GWA) study of type 2 diabetes in adults. We examined the effects of two perfect surrogates for this SNP plus 11 other SNPs at this locus with respect to our childhood obesity cohort, consisting of both Caucasians and African Americans (AA). Utilizing data from our ongoing GWA study in our cohort of 418 Caucasian obese children (BMI$95th percentile), 2,270 Caucasian controls (BMI,95th percentile), 578 AA obese children and 1,424 AA controls, we investigated the association of the previously reported variation at the FTO locus with the childhood form of this disease in both ethnicities. The minor allele frequencies (MAF) of rs8050136 and rs3751812 (perfect surrogates for rs9939609 i.e. both r2 = 1) in the Caucasian cases were 0.448 and 0.443 respectively while they were 0.391 and 0.386 in Caucasian controls respectively, yielding for both an odds ratio (OR) of 1.27 (95% CI 1.08–1.47; P = 0.0022). Furthermore, the MAFs of rs8050136 and rs3751812 in the AA cases were 0.449 and 0.115 respectively while they were 0.436 and 0.090 in AA controls respectively, yielding an OR of 1.05 (95% CI 0.91–1.21; P = 0.49) and of 1.31 (95% CI 1.050–1.643; P = 0.017) respectively. Investigating all 13 SNPs present on the Illumina HumanHap550 BeadChip in this region of linkage disequilibrium, rs3751812 was the only SNP conferring significant risk in AA. We have therefore replicated and refined the association in an AA cohort and distilled a tag-SNP, rs3751812, which captures the ancestral origin of the actual mutation. As such, variants in the FTO gene confer a similar magnitude of risk of obesity to children as to their adult counterparts and appear to have a global impact.
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    Erratum to: AGC1 Deficiency Causes Infantile Epilepsy, Abnormal Myelination, and Reduced N-Acetylaspartate
    (2014) Otieno, F. G.; Falk, M.J.; Li, D.; Gai, X.; McCormick, E.; Place, E.; Lasorsa, F.M.; Hou, C.; Kim, C.E.; Abdel-Magid, N.; Vazquez, L.; Mentch, F.D.; Chiavacci, R. M.; Liang, J.; Liu, X.; Jiang, H.; Giannuzzi, G.; Marsh, E.D.; Yiran, G.; Tian, L.; Palmieri, F.; Hakonarson, H.
    BACKGROUND: Whole exome sequencing (WES) offers a powerful diagnostic tool to rapidly and efficiently sequence all coding genes in individuals presenting for consideration of phenotypically and genetically heterogeneous disorders such as suspected mitochondrial disease. Here, we report results of WES and functional validation in a consanguineous Indian kindred where two siblings presented with profound developmental delay, congenital hypotonia, refractory epilepsy, abnormal myelination, fluctuating basal ganglia changes, cerebral atrophy, and reduced N-acetylaspartate (NAA). METHODS: Whole blood DNA from one affected and one unaffected sibling was captured by Agilent SureSelect Human All Exon kit and sequenced on the Illumina HiSeq2000. Mutations were validated by Sanger sequencing in all family members. Protein from wild-type and mutant fibroblasts was isolated to assess mutation effects on protein expression and enzyme activity. RESULTS: A novel SLC25A12 homozygous missense mutation, c.1058G>A; p.Arg353Gln, segregated with disease in this kindred. SLC25A12 encodes the neuronal aspartate-glutamate carrier 1 (AGC1) protein, an essential component of the neuronal malate/aspartate shuttle that transfers NADH and H(+) reducing equivalents from the cytosol to mitochondria. AGC1 activity enables neuronal export of aspartate, the glial substrate necessary for proper neuronal myelination. Recombinant mutant p.Arg353Gln AGC1 activity was reduced to 15% of wild type. One prior reported SLC25A12 mutation caused complete loss of AGC1 activity in a child with epilepsy, hypotonia, hypomyelination, and reduced brain NAA. CONCLUSIONS: These data strongly suggest that SLC25A12 disease impairs neuronal AGC1 activity. SLC25A12 sequencing should be considered in children with infantile epilepsy, congenital hypotonia, global delay, abnormal myelination, and reduced brain NAA.
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    A Novel Susceptibility Locus for Type 1 Diabetes on Chr12q13 Identified by a Genome-Wide Association Study
    (American Diabetes Association, 2008-04) Hakonarson, H.; Qu, H.; Bradfield, J. P.; Marchand, L.; Kim, C. E.; Glessner, J. T.; Grabs, R.; Casalunovo, T.; Taback, S. P.; Frackelton, E. C.; Eckert, A. W.; Annaiah, K.; Lawson, M. L.; Otieno, George Ochieng; Santa, E.; Shaner, J. L.; Smith, R. M.; Onyiah, C. C.; Skraban, R.; Chiavacci, R. M.; Robinson, L. J.; Stanley, C. A.; Kirsch, S. E.; Devoto, M.; Monos, D. S.; Grant, S. F. A.; Polychronakos, C.
    OBJECTIVE—In stage 1 of our genome-wide association (GWA) study for type 1 diabetes, one locus at 16p13 was detected (P = 1.03 × 10−10) and confirmed in two additional cohorts. Here we describe the results of testing, in these additional cohorts, 23 loci that were next in rank of statistical significance. RESEARCH DESIGN AND METHODS—Two independent cohorts were studied. The Type 1 Diabetes Genetics Consortium replication cohort consisted of 549 families with at least one child diagnosed with diabetes (946 total affected) and DNA from both parents. The Canadian replication cohort consisted of 364 nuclear family trios with one type 1 diabetes–affected offspring and two parents (1,092 individuals). RESULTS—One locus at 12q13, with the highest statistical significance among the 23, was confirmed. It involves type 1 diabetes association with the minor allele of rs1701704 (P = 9.13 × 10−10, OR 1.25 [95% CI 1.12–1.40]). CONCLUSIONS—We have discovered a type 1 diabetes locus at 12q13 that is replicated in an independent cohort of type 1 diabetic patients and confers a type 1 diabetes risk comparable with that of the 16p13 locus we recently reported. These two loci are identical to two loci identified by the whole-genome association study of the Wellcome Trust Case-Control Consortium, a parallel independent discovery that adds further support to the validity of the GWA approach
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    ORMDL3 variants associated with asthma susceptibility in North Americans of European ancestry
    (Elsevier, 2008-12) Sleiman, P. M. A.; Annaiah, K.; Imielinski, M.; Bradfield, J. P.; Kim, C. E.; Frackelton, E. C.; Glessner, J. T.; Eckert, A. W.; Otieno, F. G.; Santa, E.; Thomas, K.; Smith, R. M.; Glaberson, W.; Garris, M.; Gunnlaugsson, S.; Chiavacci, R. M.; Allen, J.; Spergel, J.; Grundmeier, R.; Grunstein, M. M.; Magnusson, M.; Bisgaard, H.; Grant, S. F. A.; Hakonarson, H.