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1.  Comparison of biological specimens and DNA collection methods for PCR amplification and microarray analysis 
PMCID: PMC3660108  PMID: 23241593
biological specimens; chromosomal microarray; DNA isolation; genotyping; PCR amplification
2.  Assessment and Treatment in Autism Spectrum Disorders: A Focus on Genetics and Psychiatry 
Autism Research and Treatment  2012;2012:242537.
Autism spectrum disorders (ASDs) are neurobehavioral disorders characterized by abnormalities in three behavioral domains including social interaction, impaired communication, and repetitive stereotypic behaviors. ASD affects approximately 1% of children and is on the rise with significant genetic mechanisms underlying these disorders. We review the current understanding of the role of genetic and metabolic factors contributing to ASD with the use of new genetic technology. Fifty percent is diagnosed with chromosomal abnormalities, small DNA deletions/duplications, single-gene conditions, or metabolic disturbances. Genetic evaluation is discussed along with psychiatric treatment and approaches for selection of medication to treat associated challenging behaviors or comorbidities seen in ASD. We emphasize the importance of prioritizing treatment based on target symptom clusters and in what order for individuals with ASD, as the treatment may vary from patient to patient.
PMCID: PMC3420490  PMID: 22934170
3.  APOA1 gene polymorphisms in the South Asian immigrant population in the United States 
Indian Journal of Human Genetics  2011;17(3):194-200.
Coronary artery disease (CAD) is a leading cause of death in the United States. South Asian immigrants (SAIs) from the Indian subcontinent living in the US are disproportionately at higher risk of CAD than other immigrant populations. Unique genetic factors may predispose SAIs to increased risk of developing CAD when adopting a Western lifestyle including a higher-fat diet, more sedentary behavior and additional gene-environment interactions. SAIs are known to have low levels of the protective high density lipoprotein (HDL) and an altered function for Apo-lipoprotein A-1 (ApoA1), the main protein component of HDL cholesterol. One gene that may be genetically distinctive in this population is APOA1 which codes for ApoA-1 protein, a potentially important contributing factor in the development of CAD.
DNA sequencing was performed to determine the status of the seven single-nucleotide polymorphisms (SNPs) in the APOA1 gene from 94 unrelated SAI adults. Genotypes, allelic frequencies, and intragenic linkage disequilibrium of the APOA1 SNPs were calculated.
Several polymorphisms and patterns were common among persons of south Asian ethnicity. Frequencies for SNPs T655C, T756C and T1001C were found to be different than those reported in European Caucasian individuals. Linkage disequilibrium was found to be present between most (13 of 15) SNP pairings indicating common inheritance patterns.
SAIs showed variability in the sequence of the APOA1 gene and linkage disequilibrium for most SNPS. This pattern of APOA1 SNPs may contribute to decreased levels of HDL cholesterol reported in SAIs, leading to an increased risk for developing CAD in this population.
PMCID: PMC3276989  PMID: 22345992
APOA1; coronary artery disease; linkage disequilibrium; single nucleotide gene polymorphisms; south Asian immigrants
4.  A 9-year-old Male with a Duplication of Chromosome 3p25.3p26.2: Clinical Report and Gene Expression Analysis 
We describe a 9-year-old male referred for genetic evaluation for Prader-Willi syndrome (PWS). PWS is the most common genetically-defined cause of life-threatening obesity and results from a functional loss of paternally-expressed genes from the chromosome 15q11-q13 region. The patient presented with pervasive developmental disorder, delayed speech and rapid onset of obesity at age 4 years, all features similar to PWS. However, chromosome 15q11-q13 methylation testing and fragile X studies were normal. GTG-banding and fluorescence in situ hybridization with whole chromosome 3 paint probe and a chromosome 3p subtelomeric probe suggested a duplication of 3p25.3p26.2, a finding supported by comparative genomic hybridization. This region of chromosome 3p contains genes which contribute to obesity and behavioral problems, most notably, ghrelin (GHRL), an oxytocin receptor (OXTR), solute carrier family 6 members (GABA neurotransmitter transporters, SLC6A1 and SLC6A11) and peroxisome proliferator-activated receptor, gamma (PPARG). To characterize these obesity and behavior related genes in our subject, we performed quantitative RT-PCR and compared expression levels with similarly aged male subjects (four nonobese males, four obese males and four PWS males - two with 15q11-q13 deletions and two with maternal disomy 15). Our studies suggest increased expression of several genes in the 3p duplication region, including GHRL and PPARG, which may contribute to the phenotypic features in our 3p duplication subject.
PMCID: PMC2568077  PMID: 16470700
obesity; pervasive developmental disorder; comparative genomic hybridization; gene expression; ghrelin (GHRL); peroxisome proliferator-activated receptor; gamma (PPARG); oxytocin receptor (OXTR); RT-PCR; Prader-Willi syndrome (PWS)
5.  X Chromosome Inactivation in Women with Alcoholism 
All female mammals with two X chromosomes balance gene expression with males having only one X by inactivating one of their Xs (X chromosome inactivation, XCI). Analysis of XCI in females offers the opportunity to investigate both X-linked genetic factors and early embryonic development that may contribute to alcoholism. Increases in the prevalence of skewing of XCI in women with alcoholism could implicate biological risk factors.
The pattern of XCI was examined in DNA isolated in blood from 44 adult females meeting DSM IV criteria for an Alcohol Use Disorder, and 45 control females with no known history of alcohol abuse or dependence. XCI status was determined by analyzing digested and undigested polymerase chain reaction (PCR) products of the polymorphic androgen receptor (AR) gene located on the X chromosome. Subjects were categorized into 3 groups based upon the degree of XCI skewness: random (50:50–64:36), moderately skewed (65:35–80:20) and highly skewed (>80:20).
XCI status from informative females with alcoholism was found to be random in 59% (n=26), moderately skewed in 27% (n=12) or highly skewed in 14% (n=6). Control subjects showed 60%, 29% and 11%, respectively. The distribution of skewed XCI observed among women with alcoholism did not differ statistically from that of control subjects (χ2 =0.14, 2 df, p=0.93).
Our data did not support an increase in XCI skewness among women with alcoholism or implicate early developmental events associated with embryonic cell loss or unequal (non-random) expression of X-linked gene(s) or defects in alcoholism among females.
PMCID: PMC3371305  PMID: 22375556
Alcoholism; Women; X Chromosome Inactivation; Skewness; AR Gene
6.  The Neuroanatomy of Genetic Subtype Differences in Prader-Willi Syndrome 
American Journal of Medical Genetics  2012;159B(2):243-253.
Despite behavioral differences between genetic subtypes of Prader-Willi syndrome, no studies have been published characterizing brain structure in these subgroups. Our goal was to examine differences in the brain structure phenotype of common subtypes of Prader-Willi syndrome (PWS) [chromosome 15q deletions and maternal uniparental disomy 15 (UPD)].
Fifteen individuals with PWS due to a typical deletion ((DEL) Type I; n=5, Type II; n=10), 8 with PWS due to UPD, and 25 age-matched healthy-weight individuals (HWC) participated in structural magnetic resonance imaging (MRI) scans. A custom voxel-based morphometry processing stream was used to examine regional differences in gray and white matter volume between groups, covarying for age, sex, and body mass index (BMI).
Overall, compared to HWC, PWS individuals had lower gray matter volumes that encompassed the prefrontal, orbitofrontal and temporal cortices, hippocampus and parahippocampal gyrus, and lower white matter volumes in the brain stem, cerebellum, medial temporal and frontal cortex. Compared to UPD, the DEL subtypes had lower gray matter volume primarily in the prefrontal and temporal cortices, and lower white matter in the parietal cortex. The UPD subtype had more extensive lower gray and white matter volumes in the orbitofrontal and limbic cortices compared to HWC.
These preliminary findings are the first structural neuroimaging findings to support potentially separate neural mechanisms mediating the behavioral differences seen in these genetic subtypes.
PMCID: PMC3296480  PMID: 22241551
chromosome 15q; hyperphagia; obesity; voxel-based morphometry; MRI
7.  Methylation-Specific Multiplex Ligation-Dependent Probe Amplification and Identification of Deletion Genetic Subtypes in Prader-Willi Syndrome 
Purpose: Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are complex neurodevelopmental disorders caused by loss of expression of imprinted genes from the 15q11-q13 region depending on the parent of origin. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) kits from MRC-Holland (Amsterdam, The Netherlands) were used to detect PWS and AS deletion subtypes. We report our experience with two versions of the MS-MLPA-PWS/AS kit (original A1 and newer B1) in determining methylation status and deletion subtypes in individuals with PWS. Methods: MS-MLPA analysis was performed on DNA isolated from a large cohort of PWS subjects with the MS-MLPA-PWS/AS-A1 and -B1 probe sets. Results: Both MS-MLPA kits will identify deletions in the 15q11-q13 region but the original MS-MLPA-A1 kit has a higher density of probes at the telomeric end of the 15q11-q13 region, which is more useful for identifying individuals with atypical deletions. The newer B1 kit contains more probes in the imprinting center (IC) and adjoining small noncoding RNAs useful in identifying small microdeletions. Conclusion: The A1 kit identified the typical deletions and smaller atypical deletions, whereas the B1 kit was more informative for identifying microdeletions including the IC and SNORD116 regions. Both kits should be made available for accurate characterization of PWS/AS deletion subtypes as well as evaluating for IC and SNORD116 microdeletions.
PMCID: PMC3306590  PMID: 21977908
8.  Mass Screening for Severe Problem Behavior among Infants and Toddlers In Peru 
Severe behavior problems among people with intellectual and developmental disabilities (IDD) are a major barrier to integration in the community. Recent research suggests that these behaviors often begin very early in life and might be prevented by early identification and intervention (Rojahn, Schroeder, & Hoch, 2008). The current paper presents a method of mass screening for early signs of severe behavior problems among infants and toddlers in Peru.
A Parental Concerns Questionnaire (PCQ) which asks 15 questions, each related to a risk factor for severe behavior problems, based on past research on IDD, was used by veteran parents to interview 341 new parents who had been solicited by TV, radio, and public service announcements across the country. Of these, 262 were recruited and enrolled in a longitudinal study in which they will be followed for 12 months, to see if at-risk children actually will develop severe behavior problems. An extensive initial interdisciplinary evaluation was given to each child. Consumer satisfaction questionnaires were given to the parents as to their attitude toward the screening method.
Data from the Interdisciplinary Evaluations of the sample suggest a very high hit rate (96%) by the screening instrument (PCQ). Consumer satisfaction was 98%, suggesting that the method was tolerated well by parents.
The PCQ is a brief and efficient method to screen infants and toddlers at risk for severe behavior problems. The data also suggest that parents suspect these problems at a very early age. Early intervention thus seems a feasible strategy to intervene before these problems become deeply ingrained as children develop.
PMCID: PMC3433073  PMID: 22962573
severe aggression; self-injurious behavior; stereotyped behavior; behavior problems; intellectual disabilities; infants and toddlers; early prevention
9.  Importance of Reward and Prefrontal Circuitry in Hunger and Satiety: Prader-Willi Syndrome vs. Simple Obesity 
The majority of research on obesity has focused primarily on clinical features (eating behavior, adiposity measures), or peripheral appetite-regulatory peptides (leptin, ghrelin). However, recent functional neuroimaging studies have demonstrated that some reward circuitry regions which are associated with appetite-regulatory hormones are also involved in the development and maintenance of obesity. Prader-Willi syndrome (PWS), characterized by hyperphagia and hyperghrelinemia reflecting multi-system dysfunction in inhibitory and satiety mechanisms, serves as an extreme model of genetic obesity. Simple (non-PWS) obesity (OB) represents an obesity control state.
This study investigated subcortical food motivation circuitry and prefrontal inhibitory circuitry functioning in response to food stimuli before and after eating in individuals with PWS compared with OB. We hypothesized that groups would differ in limbic regions (i.e., hypothalamus, amygdala) and prefrontal regions associated with cognitive control [i.e., dorsolateral prefrontal cortex (DLPFC), orbitofrontal cortex (OFC)] after eating.
Design and Participants
Fourteen individuals with PWS, 14 BMI- and age-matched individuals with OB, and 15 age-matched healthy-weight controls (HWC) viewed food and non-food images while undergoing functional MRI before (pre-meal) and after (post-meal) eating. Using SPM8, group contrasts were tested for hypothesized regions: hypothalamus, nucleus accumbens (NAc), amygdala, hippocampus, OFC, medial PFC, and DLPFC.
Compared with OB and HWC, PWS demonstrated higher activity in reward/limbic regions (NAc, amygdala) and lower activity in hypothalamus and hippocampus, in response to food (vs. non-food) images pre-meal. Post-meal, PWS exhibited higher subcortical activation (hypothalamus, amygdala, hippocampus) compared to OB and HWC. OB showed significantly higher activity versus PWS and HWC in cortical regions (DLPFC, OFC) associated with inhibitory control.
In PWS compared with obesity per se, results suggest hyperactivations in subcortical reward circuitry and hypoactivations in cortical inhibitory regions after eating, which provides evidence of neural substrates associated with variable abnormal food motivation phenotypes in PWS and simple obesity.
PMCID: PMC3270121  PMID: 22024642
obesity; DLPFC; inhibition; motivation; fMRI; Prader-Willi syndrome
10.  Umbilical cord blood banking: an update 
Umbilical cord blood is a potential vast source of primitive hematopoietic stem and progenitor cells available for clinical application to reconstitute the hematopoietic system and/or restore immunological function in affected individuals requiring treatment. Cord blood can be used as an alternative source for bone marrow transplantation and its use is developing into a new field of treatment for pediatric and adult patients presenting with hematological disorders, immunological defects and specific genetic diseases.
More than 25,000 allogeneic cord blood transplantations have been performed worldwide since the first cord blood transplantation in 1988. There are two banking options for storing umbilical cord blood [private (family) and public]. Cord blood stored in private banks are used for either autologous or allogeneic transplants for the infant donor or related family members but private cord blood banks are not searchable or available to the public. More than 780,000 cord blood units are stored in over 130 private cord blood banks, worldwide, and over 400,000 units in more than 100 quality controlled public cord blood banks.
Researchers continue to evaluate the usefulness of cord blood cells in treating human diseases or disorders for purposes other than hematological disorders including heart disease, strokes, brain or spinal cord injuries and cancer. This review summarizes the status of umbilical cord blood banking, its history and current and potential use in the treatment of human disease.
PMCID: PMC3170109  PMID: 21617932
Umbilical cord blood; Public and private cord blood banks; Transplantation; Clinical applications; Regenerative medicine
11.  TPH2 G/T polymorphism is associated with hyperphagia, IQ, and internalizing problems in Prader-Willi syndrome 
Prader-Willi syndrome (PWS) is a genetic, neurodevelopmental disorder characterized by intellectual disabilities, growth hormone dysregulation, hyperphagia, increased risks of morbid obesity, compulsive behaviors, and irritability. As aberrant serotonergic functioning is strongly implicated in PWS, we examined associations between the PWS phenotype and polymorphisms in tryptophan hydroxylase 2 (TPH2), the rate-limiting enzyme in the biosynthesis of serotonin in the brain.
92 individuals with PWS aged 4 to 50 years (M = 21.97) were genotyped for the TPH2 G703-T polymorphism. IQ testing was conducted in offspring, and parents completed questionnaires that tapped their child’s compulsivity, hyperphagia, and other behavior problems.
As expected, the frequency of G/T or T/T polymorphisms in participants with PWS (39%) was similar to rates found in the general population (38%). Compared to those with a homozygous (G/G) genotype, individuals with a T allele had significantly higher hyperphagic behavior, drive, and severity scores, and they also had a younger age of onset of hyperphagia. Those with a T allele also had higher IQ scores than their counterparts. Females with a T allele had significantly higher internalizing symptoms, primarily anxiety and depression, than all others.
TPH2 G/T polymorphisms, and presumed loss of enzyme function, were associated with specific aspects of the PWS phenotype. Aberrant serotonergic functioning is strongly implicated in hyperphagia in PWS, and females with TPH2 T alleles may be at higher risk for affective or mood disorders. Findings hold promise for examining other serotonin-altering genes in PWS, and for future serotonin-altering treatment trials.
PMCID: PMC3353323  PMID: 21418060
12.  Growth Standards of Infants With Prader-Willi Syndrome 
Pediatrics  2011;127(4):687-695.
To generate and report standardized growth curves for weight, length, head circumference, weight/length, and BMI for non–growth hormone–treated white infants (boys and girls) with Prader-Willi syndrome (PWS) between 0 and 36 months of age. The goal was to monitor growth and compare data with other infants with PWS.
Anthropometric measures (N = 758) were obtained according to standard methods and analyzed from 186 non–growth hormone–treated white infants (108 boys and 78 girls) with PWS between 0 and 36 months of age. Standardized growth curves were developed and the 3rd, 10th, 25th, 50th, 75th, 90th, and 97th percentiles were calculated by using the LMS (refers to λ, μ, and σ) smoothing procedure method for weight, length, head circumference, weight/length, and BMI along with the normative 50th percentile using Centers for Disease Control and Prevention national growth data from 2003. The data were plotted for comparison purposes.
Five separate standardized growth curves (weight, length, head circumference, weight/length, and BMI) representing 7 percentile ranges were developed from 186 non–growth hormone–treated white male and female infants with PWS aged 0 to 36 months, and the normative 50th percentile was plotted on each standardized infant growth curve.
We encourage the use of these growth standards when examining infants with PWS and evaluating growth for comparison purposes, monitoring for growth patterns, nutritional assessment, and recording responses to growth hormone therapy, commonly used in infants and children with PWS.
PMCID: PMC3065075  PMID: 21402637
Prader-Willi syndrome; standardized growth curves; obesity; growth hormone therapy
13.  Nutritional Phases in Prader–Willi Syndrome 
Prader–Willi syndrome (PWS) is a complex neurobehavioral condition which has been classically described as having two nutritional stages: poor feeding, frequently with failure to thrive (FTT) in infancy (Stage 1), followed by hyperphagia leading to obesity in later childhood (Stage 2). We have longitudinally followed the feeding behaviors of individuals with PWS and found a much more gradual and complex progression of the nutritional phases than the traditional two stages described in the literature. Therefore, this study characterizes the growth, metabolic, and laboratory changes associated with the various nutritional phases of PWS in a large cohort of subjects. We have identified a total of seven different nutritional phases, with five main phases and sub-phases in phases 1 and 2. Phase 0 occurs in utero, with decreased fetal movements and growth restriction compared to unaffected siblings. In phase 1 the infant is hypotonic and not obese, with sub-phase 1a characterized by difficulty feeding with or without FTT (ages birth—15 months; median age at completion: 9 months). This phase is followed by sub-phase 1b when the infant grows steadily along a growth curve and weight is increasing at a normal rate (median age of onset: 9 months; age quartiles 5–15 months). Phase 2 is associated with weight gain—in sub-phase 2a the weight increases without a significant change in appetite or caloric intake (median age of onset 2.08 years; age quartiles 20–31 months;), while in sub-phase 2b the weight gain is associated with a concomitant increased interest in food (median age of onset: 4.5 years; quartiles 3–5.25 years). Phase 3 is characterized by hyperphagia, typically accompanied by food-seeking and lack of satiety (median age of onset: 8 years; quartiles 5–13 years). Some adults progress to phase 4 which is when an individual who was previously in phase 3 no longer has an insatiable appetite and is able to feel full. Therefore, the progression of the nutritional phases in PWS is much more complex than previously recognized. Awareness of the various phases will aid researchers in unraveling the pathophysiology of each phase and provide a foundation for developing rational therapies. Counseling parents of newly diagnosed infants with PWS as to what to expect with regard to these nutritional phases may help prevent or slow the early-onset of obesity in this syndrome.
PMCID: PMC3285445  PMID: 21465655
Prader–Willi; nutrition; appetite; weight gain
14.  Genetics and Mitochondrial Abnormalities in Autism Spectrum Disorders: A Review 
Current Genomics  2011;12(5):322-332.
We review the current status of the role and function of the mitochondrial DNA (mtDNA) in the etiology of autism spectrum disorders (ASD) and the interaction of nuclear and mitochondrial genes. High lactate levels reported in about one in five children with ASD may indicate involvement of the mitochondria in energy metabolism and brain development. Mitochondrial disturbances include depletion, decreased quantity or mutations of mtDNA producing defects in biochemical reactions within the mitochondria. A subset of individuals with ASD manifests copy number variation or small DNA deletions/duplications, but fewer than 20 percent are diagnosed with a single gene condition such as fragile X syndrome. The remaining individuals with ASD have chromosomal abnormalities (e.g., 15q11-q13 duplications), other genetic or multigenic causes or epigenetic defects. Next generation DNA sequencing techniques will enable better characterization of genetic and molecular anomalies in ASD, including defects in the mitochondrial genome particularly in younger children.
PMCID: PMC3145262  PMID: 22294875
Autism spectrum disorders (ASD); mitochondrial DNA (mtDNA) mutations and depletion; oxidative stress; nuclear genes; lactate/pyruvate ratios; genetic causation.
15.  Apo Lipoprotein A1 Gene Polymorphisms Predict Cardio-Metabolic Risk in South Asian Immigrants 
Disease markers  2012;32(1):9-19.
Objectives: Coronary artery disease (CAD) is a leading cause of death globally with increasing burden in South Asians in the US. Specific genetic variants that influence CAD have not been fully assessed in South Asian Immigrants. The goal is to identify Apo lipoprotein A1 (APOA1) gene polymorphisms and their association with CAD risk factors, metabolic syndrome and dysfunctional HDL (Dys-HDL).
Methods: A community-based study on South Asians aged 35-65 years without CAD was conducted. APOA1 gene sequencing was performed and genotypes compared with cardiovascular findings.
Results: The prevalence of metabolic syndrome and dysfunctional-HDL was 29.7% and 26%, respectively. Six novel APOA1 gene single nucleotide peptides (SNPs) were analyzed. Three of the six SNPs (G2, G3, and G5) were found to be associated with metabolic syndrome; G2 (T655C) (p=0.044), G3 (T756C) (p=0.037) and G5 (T1001C) (p=0.037). APOA1 gene SNP G1 (T319C) was highly correlated with low HDL levels (p=0.001). In our study, both associations of APOA1 SNPs with metabolic syndrome and low HDL remained after age-adjustment.
Conclusion: Discovery of novel gene polymorphisms will help to understand further the causes of excess CAD risk in South Asians so that preventative strategies targeted to high-risk group can be developed.
PMCID: PMC3826425  PMID: 22297598
Coronary artery disease; risk factors; South Asian immigrants; polymorphisms; Apo Lipoprotein A1; dysfunctional high density lipoprotein
16.  Deaths Due to Choking in Prader-Willli Syndrome 
Prader-Willi syndrome (PWS) is the most common known syndromic cause of life threatening obesity, yet few studies have examined the causes of death in PWS. The objective of this study was to examine the contribution of choking leading to mortality in PWS. In 1999, a brief survey was made available from the Prader-Willi Syndrome Association (USA) bereavement program, which documented demographic data and causes of death. Families were subsequently offered the opportunity to fill out a detailed questionnaire and additional forms to release medical records. Demographic information was available on 178 deceased individuals with PWS, and cause of death available on 152 individuals. Fifty-four families completed questionnaires. Of the deceased individuals with completed questionnaires, 34% reported a history of choking. Choking was listed by familial report as the cause of death in 12 (7.9%) of 152 subjects with an average age of 24 years (range 3–52y; median 22.5y) at death from choking. Only two of these individuals were less than eight years of age. The data suggest that risks associated with choking are different in the PWS population compared with normal. Potential causes of increased choking in PWS include poor oral/motor coordination, poor gag reflex, hypotonia, hyperphagia, decreased mastication and voracious feeding habits. We recommend implementation of preventive measures and education for families and group home care providers for all individuals with PWS including the Heimlich maneuver, supervised meals, better food preparation and diet modification to avoid high risk choking items.
PMCID: PMC3243066  PMID: 17036318
Prader-Willi syndrome; choking; aspiration; mortality; sudden death; vomiting
17.  Gastric Rupture and Necrosis in Prader-Willi Syndrome 
Hyperphagia and obesity are common features in individuals with Prader-Willi syndrome (PWS). Demographic and cause of death data from individuals with PWS were obtained through a national support organization. Four reports of unexpected mortality due to gastric rupture and necrosis were found in 152 reported deaths, accounting for 3% of the causes of mortality. Four additional individuals were suspected to have gastric rupture. Vomiting and abdominal pain, although rare in PWS, were frequent findings in this cohort. The physician should consider an emergent evaluation for gastric rupture and necrosis in individuals with PWS who present with vomiting and abdominal pain.
PMCID: PMC3241991  PMID: 17667731
Prader-Willi syndrome; gastric necrosis; gastric perforation; vomiting; hyperphagia; mortality
18.  Genomics of Childhood Obesity 
Current Genomics  2011;12(3):153.
PMCID: PMC3137000  PMID: 22043163
19.  Prader-Willi Syndrome: Obesity due to Genomic Imprinting 
Current Genomics  2011;12(3):204-215.
Prader-Willi syndrome (PWS) is a complex neurodevelopmental disorder due to errors in genomic imprinting with loss of imprinted genes that are paternally expressed from the chromosome 15q11-q13 region. Approximately 70% of individuals with PWS have a de novo deletion of the paternally derived 15q11-q13 region in which there are two subtypes (i.e., larger Type I or smaller Type II), maternal disomy 15 (both 15s from the mother) in about 25% of cases, and the remaining subjects have either defects in the imprinting center controlling the activity of imprinted genes or due to other chromosome 15 rearrangements. PWS is characterized by a particular facial appearance, infantile hypotonia, a poor suck and feeding difficulties, hypogonadism and hypogenitalism in both sexes, short stature and small hands and feet due to growth hormone deficiency, mild learning and behavioral problems (e.g., skin picking, temper tantrums) and hyperphagia leading to early childhood obesity. Obesity is a significant health problem, if uncontrolled. PWS is considered the most common known genetic cause of morbid obesity in children. The chromosome 15q11-q13 region contains approximately 100 genes and transcripts in which about 10 are imprinted and paternally expressed. This region can be divided into four groups: 1) a proximal non-imprinted region; 2) a PWS paternal-only expressed region containing protein-coding and non-coding genes; 3) an Angelman syndrome region containing maternally expressed genes and 4) a distal non-imprinted region. This review summarizes the current understanding of the genetic causes, the natural history and clinical presentation of individuals with PWS.
PMCID: PMC3137005  PMID: 22043168
Prader-Willi syndrome; Angelman syndrome; genomic imprinting; deletion; maternal disomy; clinical presentation and differences; genetic subtypes.
20.  Metabolic syndrome in South Asian immigrants: more than low HDL requiring aggressive management 
Aggressive clinical and public health interventions have resulted in significant reduction in coronary artery disease (CAD) worldwide. However, South Asian immigrants (SAIs) exhibit the higher prevalence of CAD and its risk factors as compared with other ethnic populations. The objective of the current study is to assess the prevalence of metabolic syndrome (MS), its association with high density Lipoprotein (HDL) function, Apo lipoprotein A-I (APOA1) gene polymorphisms, and sub-clinical CAD using common carotid intima-media thickness (CCA-IMT) as a surrogate marker. A community-based cross-sectional study was conducted on SAIs aged 35-65 years. Dysfunctional/pro-inflammatory (Dys-HDL) was determined using novel cell free assay and HDL inflammatory index. Six intronic APOA1 gene polymorphisms were analyzed by DNA sequencing. According to the International Diabetes Federation definition, MS prevalence was 29.7% in SAIs without CAD and 26% had HDL inflammatory index ≥ 1 suggesting pro-inflammatory Dys-HDL. Six novel APOA1 single nucleotide polymorphisms (SNPs) were analyzed with logistic regression, three SNPs (G2, G3, and G5) were found to be significantly associated with MS (p = 0.039, p = 0.038, p = 0.054). On multi-variate analysis, MS was significantly associated with BMI > 23 (P = 0.005), Apo-A-I levels (p = 0.01), and Lp [a] (p < 0.0001). SAIs are known to be at a disproportionately high risk for CAD that may be attributed to a high burden for MS. There is need to explore and understand non-traditional risk factors with special focus on Dys-HDL, knowing that SAIs have low HDL levels. Large prospective studies are needed to further strengthen current study results.
PMCID: PMC3076254  PMID: 21410987
21.  An Interstitial 15q11-q14 Deletion: Expanded Prader-Willi Syndrome Phenotype 
We present an infant girl with a de novo interstitial deletion of the chromosome 15q11-q14 region, larger than the typical deletion seen in Prader-Willi syndrome (PWS). She presented with features seen in PWS including hypotonia, a poor suck, feeding problems and mild micrognathia. She also presented with features not typically seen in PWS such as preauricular ear tags, a high arched palate, edematous feet, coarctation of the aorta, a PDA and a bicuspid aortic valve. G-banded chromosome analysis showed a large de novo deletion of the proximal long arm of chromosome 15 confirmed using FISH probes (D15511 and GABRB3). Methylation testing was abnormal and consistent with the diagnosis of PWS. Because of the large appearing deletion by karyotype analysis, an array comparative genomic hybridization (CGH) was performed. A 12.3 Mb deletion was found which involved the 15q11-q14 region containing approximately 60 protein coding genes. This rare deletion was approximately twice the size of the typical deletion seen in PWS and involved the proximal breakpoint BP1 and the distal breakpoint was located in the 15q14 band between previously recognized breakpoints BP5 and BP6. The deletion extended slightly distal to the AVEN gene including the neighboring CHRM5 gene. There is no evidence that the genes in the 15q14 band are imprinted; therefore, their potential contribution in this patient's expanded Prader-Willi syndrome phenotype must be a consequence of dosage sensitivity of the genes or due to altered expression of intact neighboring genes from a position effect.
PMCID: PMC2814996  PMID: 20082457
de novo interstitial 15q11-q14 deletion; expanded PWS phenotype; array CGH; genotype-phenotype correlations
22.  Gene expression in cardiac tissues from infants with idiopathic conotruncal defects 
Tetralogy of Fallot (TOF) is the most commonly observed conotruncal congenital heart defect. Treatment of these patients has evolved dramatically in the last few decades, yet a genetic explanation is lacking for the failure of cardiac development for the majority of children with TOF. Our goal was to perform genome wide analyses and characterize expression patterns in cardiovascular tissue (right ventricle, pulmonary valve and pulmonary artery) obtained at the time of reconstructive surgery from 19 children with tetralogy of Fallot.
We employed genome wide gene expression microarrays to characterize cardiovascular tissue (right ventricle, pulmonary valve and pulmonary artery) obtained at the time of reconstructive surgery from 19 children with TOF (16 idiopathic and three with 22q11.2 deletions) and compared gene expression patterns to normally developing subjects.
We detected a signal from approximately 26,000 probes reflecting expression from about half of all genes, ranging from 35% to 49% of array probes in the three tissues. More than 1,000 genes had a 2-fold change in expression in the right ventricle (RV) of children with TOF as compared to the RV from matched control infants. Most of these genes were involved in compensatory functions (e.g., hypertrophy, cardiac fibrosis and cardiac dilation). However, two canonical pathways involved in spatial and temporal cell differentiation (WNT, p = 0.017 and Notch, p = 0.003) appeared to be generally suppressed.
The suppression of developmental networks may represent a remnant of a broad malfunction of regulatory pathways leading to inaccurate boundary formation and improper structural development in the embryonic heart. We suggest that small tissue specific genomic and/or epigenetic fluctuations could be cumulative, leading to regulatory network disruption and failure of proper cardiac development.
PMCID: PMC3023653  PMID: 21208432
23.  Genomic imprinting disorders in humans: a mini-review 
Mammals inherit two complete sets of chromosomes, one from the father and one from the mother, and most autosomal genes are expressed from both maternal and paternal alleles. Imprinted genes show expression from only one member of the gene pair (allele) and their expression are determined by the parent during production of the gametes. Imprinted genes represent only a small subset of mammalian genes that are present but not imprinted in other vertebrates. Genomic imprints are erased in both germlines and reset accordingly; thus, reversible depending on the parent of origin and leads to differential expression in the course of development. Genomic imprinting has been studied in humans since the early 1980’s and accounts for several human disorders. The first report in humans occurred in Prader-Willi syndrome due to a paternal deletion of chromosome 15 or uniparental disomy 15 (both chromosome 15s from only one parent) and similar genetic disturbances were reported later in Angelman syndrome.
PMCID: PMC2788689  PMID: 19844787
Genomic imprinting; Human disorders; Assisted reproductive technology; DNA methylation; Prader-Willi syndrome; Angelman syndrome; Silver-Russell syndrome; Beckwith-Wiedemann syndrome; Albright hereditary osteodystrophy; Uniparental disomy 14
24.  TPH2 polymorphisms and expression in Prader-Willi syndrome subjects with differing genetic subtypes 
Prader-Willi syndrome (PWS) is a genetic imprinting disease that causes developmental and behavioral disturbances resulting from loss of expression of genes from the paternal chromosome 15q11-q13 region. In about 70% of subjects, this portion of the paternal chromosome is deleted, while 25% have two copies of the maternal chromosome 15, or uniparental maternal disomy (UPD; the remaining subjects have imprinting center defects. There are several documented physical and behavioral differences between the two major PWS genetic subtypes (deletion and UPD) indicating the genetic subtype plays a role in clinical presentation. Serotonin is known to be disturbed in PWS and affects both eating behavior and compulsion, which are reported to be abnormal in PWS. We investigated the tryptophan hydroxylase gene (TPH2), the rate-limiting enzyme in the production of brain serotonin, by analyzing three different TPH2 gene polymorphisms, transcript expression, and correlation with PWS genetic subtype. DNA and RNA from lymphoblastoid cell lines derived from 12 PWS and 12 comparison subjects were used for the determination of genetic subtype, TPH2 polymorphisms and quantitative RT-PCR analysis. A similar frequency of TPH2 polymorphisms was seen in the PWS and comparison subjects with PWS deletion subjects showing increased expression with one or more TPH2 polymorphism. Both PWS deletion and PWS UPD subjects had significantly lower TPH2 expression than control subjects and PWS deletion subjects had significantly lower TPH2 expression compared with PWS UPD subjects. PWS subjects with 15q11-q13 deletions had lower TPH2 expression compared with PWS UPD or control subjects, requiring replication and further studies to identify the cause including identification of disturbed gene interactions resulting from the deletion process.
PMCID: PMC3164046  PMID: 22127900
Prader-Willi syndrome; TPH2 polymorphisms and expression; Serotonin; Genetic subtypes
25.  Is gestation in Prader-Willi syndrome affected by the genetic subtype? 
Prader-Willi syndrome (PWS) is a complex genetic disorder with errors in genomic imprinting, generally due to a paternal deletion of chromosome 15q11-q13 region. Maternal disomy 15 (both 15s from the mother) is the second most common form of PWS resulting from a trisomic zygote followed by trisomy rescue in early pregnancy and loss of the paternal chromosome 15. However, trisomy 15 or mosaicism for trisomy 15 may be present in the placenta possibly leading to placental abnormalities affecting gestational age and delivery.
Methods and Subjects
We examined growth and gestational data from 167 PWS infants (93 males and 74 females; 105 infants with 15q11-q13 deletion and 62 infants with maternal disomy 15) to determine if there are differences in gestation between the two genetic subtypes.
No significant differences in growth data (birth weight, length, head circumference) or average gestational ages were found between the two genetic subgroups. However, post-term deliveries (> 42 weeks gestation) were more common in the maternal disomy group (i.e., 12 of 62 infants) compared with the deletion group (i.e., 7 of 105 infants) (chi-square test = 6.22; p < 0.02). The distribution of gestational ages in the 15q11-q13 deletion group was more bell-shaped or normal while the distribution in the maternal disomy group suggested a bimodal pattern.
Maternal disomy 15 in PWS may contribute to disturbances in gestational age and delivery by impacting on placental structure or function secondary to the abnormal chromosomal number in the placental cells or in mechanisms leading to the maternal disomy status in PWS infants.
PMCID: PMC2767487  PMID: 19760168
Prader-Willi syndrome; Maternal disomy 15; Trisomy rescue; Genomic imprinting; Abnormal gestation

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