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1.  Evaluation of utero-placental and fetal hemodynamic parameters throughout gestation in pregnant mice using high-frequency ultrasound 
Ultrasound in medicine & biology  2013;40(2):351-360.
Changes throughout gestation of maternal and fetal Doppler parameters in pregnant mice, similar to those obtained in human fetuses, using a high frequency ultrasound with a 55 MHz linear probe are described. The uterine arteries (UtA), fetal umbilical (UA) and fetal ductus venosus (DV) showed: increased peak systolic velocity (UtA, p=0.04; UA, p=0.0004; DV, p=0.02), reduced end diastolic velocity (UtA, p<0.001; UA, p<.0001; DV, p=0.01), and reduced resistance index (UtA, p=0.0004; UA, p=0.0001; DV, p=0.04) toward the end of pregnancy. The middle cerebral (MCA) and carotid arteries (CAR) showed reduced end diastolic velocity (MCA, p=0.02; CAR, p<0.0001), and resistance index (both vessels, p<0.0001). The umbilical vein showed a reduction in the pulsatile pattern (p<0.05). Increased velocities and reduced resistance index suggest a progressive increment in blood flow to the fetal mouse towards the end of pregnancy. Evaluation of fetal and utero-placental vascular parameters in CD-1 mice can be reliably performed using high frequency ultrasound.
doi:10.1016/j.ultrasmedbio.2013.09.026
PMCID: PMC4179107  PMID: 24342911
Doppler; experimental mouse model; pregnancy; high frequency ultrasound
2.  Identification of a new BRCA2 large genomic deletion associated with high risk male breast cancer 
Background
Male breast cancer (MBC) is an uncommon disease that has been the focus of limited research. It is estimated that approximately 10% of men with breast cancer have a genetic predisposition, with BRCA2 being the most prevalent genetic mutation. Here we describe the case of MBC in a 64-year-old man who presented on physical examination a nodule in his left breast and declared to have an extensive family history of cancer.
Methods and results
The patient was firstly diagnosed with an invasive ductal carcinoma (IDC) with histological grade III, nuclear grade 3, pT4N2Mx and positive for hormonal receptors and HER2. Exome sequencing was performed by massive parallel sequencing which had detected a novel BRCA2 germline mutation that is a large genomic deletion of 3,492 nucleotides including BRCA2 exon 14, and this deletion is out of frame and is predicted to lead to a stop codon in exon 15 at codon 2,496.
Conclusion
Large rearrangements in BRCA1 and BRCA2 occur in a small percentage (<1%) of patients tested for hereditary breast and ovarian cancer. This is the first report of the mutation del3492 in BRCA2 exon 14, which leads to a truncated protein and therefore is clinically relevant. Mutation segregation analysis should be further done in the Brazilian population. Herein we highlight the importance of next-generation sequencing in the detection of large genomic deletions.
doi:10.1186/s13053-014-0022-x
PMCID: PMC4308828  PMID: 25632310
Male Breast Cancer (MBC); BRCA2 mutation; Next-generation sequencing; Large genomic deletion
3.  Inherited predisposition to breast cancer among African American women 
African Americans have a disproportionate burden of aggressive young-onset breast cancer. Genomic testing for inherited predisposition to breast cancer is increasingly common in clinical practice, but comprehensive mutation profiles remain unknown for most minority populations. We evaluated 289 patients who self-identified as African American with primary invasive breast cancer and with personal or family cancer history or tumor characteristics associated with high genetic risk for all classes of germline mutations in known breast cancer susceptibility genes using a validated targeted capture and multiplex sequencing approach. Sixty-eight damaging germline mutations were identified in 65 (22 %, 95 % CI 18–28 %) of the 289 subjects. Proportions of patients with unequivocally damaging mutations in a breast cancer gene were 26 % (47/180; 95 % confident interval [CI] 20–33 %) of those with breast cancer diagnosis before age 45; 25 % (26/103; 95 % CI 17–35 %) of those with triple-negative breast cancer (TNBC); 29 % (45/156; 95 % CI 22–37 %) of those with a first or second degree relative with breast cancer before age 60 or with ovarian cancer; and 57 % (4/7; 95 % CI 18–90 %) of those with both breast and ovarian cancer. Of patients with mutations, 80 % (52/65) carried mutations in BRCA1 and BRCA2 genes and 20 % (13/65) carried mutations in PALB2, CHEK2, BARD1, ATM, PTEN, or TP53. The mutational allelic spectrum was highly heterogeneous, with 57 different mutations in 65 patients. Of patients meeting selection criteria other than family history (i.e., with young age at diagnosis or TNBC), 48 % (64/133) had very limited information about the history of cancer in previous generations of their families. Mutations in BRCA1 and BRCA2 or another breast cancer gene occur in one in four African American breast cancer patients with early onset disease, family history of breast or ovarian cancer, or TNBC. Each of these criteria defines patients who would benefit from genomic testing and novel therapies targeting DNA repair pathways.
doi:10.1007/s10549-014-3195-0
PMCID: PMC4298662  PMID: 25428789
Breast cancer; Next-generation sequencing; African American; Inherited susceptibility
4.  Spatial and Temporal Mapping of De novo Mutations in Schizophrenia To a Fetal Prefrontal Cortical Network 
Cell  2013;154(3):518-529.
SUMMARY
Genes disrupted in schizophrenia may be revealed by de novo mutations in affected persons from otherwise healthy families. Furthermore, during normal brain development, genes are expressed in patterns specific to developmental stage and neuroanatomical structure. We identified de novo mutations in persons with schizophrenia, then mapped the responsible genes onto transcriptome profiles of normal human brain tissues from age 13 weeks gestation to adulthood. In the dorsolateral and ventrolateral prefrontal cortex during fetal development, genes harboring damaging de novo mutations in schizophrenia formed a network significantly enriched for transcriptional co-expression and protein interaction. The 50 genes in the network function in neuronal migration, synaptic transmission, signaling, transcriptional regulation, and transport. These results suggest that disruptions of fetal prefrontal cortical neurogenesis are critical to the pathophysiology of schizophrenia. These results also support the feasibility of integrating genomic and transcriptome analyses to map critical neurodevelopmental processes in time and space in the brain.
doi:10.1016/j.cell.2013.06.049
PMCID: PMC3894107  PMID: 23911319
5.  SGCE mutations cause psychiatric disorders: clinical and genetic characterization 
Brain : a journal of neurology  2013;136(0 1):294-303.
Myoclonus dystonia syndrome is a childhood onset hyperkinetic movement disorder characterized by predominant alcohol responsive upper body myoclonus and dystonia. A proportion of cases are due to mutations in the maternally imprinted SGCE gene. Previous studies have suggested that patients with SGCE mutations may have an increased rate of psychiatric disorders. We established a cohort of patients with myoclonus dystonia syndrome and SGCE mutations to determine the extent to which psychiatric disorders form part of the disease phenotype. In all, 89 patients with clinically suspected myoclonus dystonia syndrome were recruited from the UK and Ireland. SGCE was analysed using direct sequencing and for copy number variants. In those patients where no mutation was found TOR1A (GAG deletion), GCH1, THAP1 and NKX2-1 were also sequenced. SGCE mutation positive cases were systematically assessed using standardized psychiatric interviews and questionnaires and compared with a disability-matched control group of patients with alcohol responsive tremor. Nineteen (21%) probands had a SGCE mutation, five of which were novel. Recruitment of family members increased the affected SGCE mutation positive group to 27 of whom 21 (77%) had psychiatric symptoms. Obsessive–compulsive disorder was eight times more likely (P < 0.001) in mutation positive cases, compulsivity being the predominant feature (P < 0.001). Generalized anxiety disorder (P = 0.003) and alcohol dependence (P = 0.02) were five times more likely in mutation positive cases than tremor controls. SGCE mutations are associated with a specific psychiatric phenotype consisting of compulsivity, anxiety and alcoholism in addition to the characteristic motor phenotype. SGCE mutations are likely to have a pleiotropic effect in causing both motor and specific psychiatric symptoms.
doi:10.1093/brain/aws308
PMCID: PMC4052887  PMID: 23365103
myoclonus dystonia; SGCE; psychiatric disorders
6.  Integration of Fall Prevention into State Policy in Connecticut 
The Gerontologist  2012;53(3):508-515.
Purpose of Study: To describe the ongoing efforts of the Connecticut Collaboration for Fall Prevention (CCFP) to move evidence regarding fall prevention into clinical practice and state policy. Methods: A university-based team developed methods of networking with existing statewide organizations to influence clinical practice and state policy. Results: We describe steps taken that led to funding and legislation of fall prevention efforts in the state of Connecticut. We summarize CCFP’s direct outreach by tabulating the educational sessions delivered and the numbers and types of clinical care providers that were trained. Community organizations that had sustained clinical practices incorporating evidence-based fall prevention were subsequently funded through mini-grants to develop innovative interventional activities. These mini-grants targeted specific subpopulations of older persons at high risk for falls. Implications: Building collaborative relationships with existing stakeholders and care providers throughout the state, CCFP continues to facilitate the integration of evidence-based fall prevention into clinical practice and state-funded policy using strategies that may be useful to others.
doi:10.1093/geront/gns122
PMCID: PMC3635855  PMID: 23042690
Polypharmacy; Connecticut Collaboration for Fall Prevention; Balance training; Visiting nurse association; Fall prevention
7.  Migrating partial seizures of infancy: expansion of the electroclinical, radiological and pathological disease spectrum 
Brain  2013;136(5):1578-1591.
Migrating partial seizures of infancy, also known as epilepsy of infancy with migrating focal seizures, is a rare early infantile epileptic encephalopathy with poor prognosis, presenting with focal seizures in the first year of life. A national surveillance study was undertaken in conjunction with the British Paediatric Neurology Surveillance Unit to further define the clinical, pathological and molecular genetic features of this disorder. Fourteen children with migrating partial seizures of infancy were reported during the 2 year study period (estimated prevalence 0.11 per 100 000 children). The study has revealed that migrating partial seizures of infancy is associated with an expanded spectrum of clinical features (including severe gut dysmotility and a movement disorder) and electrographic features including hypsarrhythmia (associated with infantile spasms) and burst suppression. We also report novel brain imaging findings including delayed myelination with white matter hyperintensity on brain magnetic resonance imaging in one-third of the cohort, and decreased N-acetyl aspartate on magnetic resonance spectroscopy. Putaminal atrophy (on both magnetic resonance imaging and at post-mortem) was evident in one patient. Additional neuropathological findings included bilateral hippocampal gliosis and neuronal loss in two patients who had post-mortem examinations. Within this cohort, we identified two patients with mutations in the newly discovered KCNT1 gene. Comparative genomic hybridization array, SCN1A testing and genetic testing for other currently known early infantile epileptic encephalopathy genes (including PLCB1 and SLC25A22) was non-informative for the rest of the cohort.
doi:10.1093/brain/awt073
PMCID: PMC3634200  PMID: 23599387
early infantile epileptic encephalopathy; migrating partial seizures in infancy; epilepsy of infancy with migrating focal seizures; malignant migrating partial epilepsy of infancy; infantile seizures
8.  Identification of a recurrent germline PAX5 mutation and susceptibility to pre-B cell acute lymphoblastic leukemia 
Nature genetics  2013;45(10):1226-1231.
doi:10.1038/ng.2754
PMCID: PMC3919799  PMID: 24013638
9.  BRCA1, TP53, and CHEK2 Germline Mutations in Uterine Serous Carcinoma 
Cancer  2012;119(2):332-338.
Background
Uterine serous carcinoma (USC) is not recognized as part of any defined hereditary cancer syndrome, and its association with hereditary breast and ovarian carcinoma and Lynch syndrome are uncertain.
Methods
Using targeted capture and massively parallel genomic sequencing, we assessed 151 subjects with USC for germline mutations in 30 tumor suppressor genes, including BRCA1, BRCA2, the DNA mismatch repair genes (MLH1, MSH2, MSH6, PMS2), TP53, and ten other genes in the Fanconi anemia (FA)-BRCA pathway. Ten cases with <10% serous histology were also assessed.
Results
Seven subjects (4.6%) carried germline loss-of-function mutations: three (2.0%) in BRCA1, two (1.3%) in TP53, and two (1.3%) in CHEK2. One subject with <10% serous histology had an MSH6 mutation. Subjects with MSH6 and TP53 mutations had neither personal nor family histories suggestive of Lynch or Li-Fraumeni syndromes. Of the 22 women with USC and a personal history of breast carcinoma, the frequency of BRCA1 mutations was 9%, compared to 0.9% in 119 women with no such history.
Conclusions
Approximately 5% of women with USC have germline mutations in three different tumor suppressor genes: BRCA1, CHEK2, and TP53. Mutations in DNA mismatch repair genes that cause Lynch syndrome are rare in USC. The germline BRCA1 mutation rate in USC subjects of 2% is higher than expected in a non-founder population, suggesting that USC is associated with hereditary breast and ovarian carcinoma in a small proportion of cases. Women with USC and breast cancer should be offered genetic testing for BRCA1 and BRCA2 mutations.
doi:10.1002/cncr.27720
PMCID: PMC3966566  PMID: 22811390
Uterine serous carcinoma; molecular genetics; BRCA1 gene; BRCA2 gene; Lynch syndrome
10.  Prevalence of Trachoma at Sub-District Level in Ethiopia: Determining When to Stop Mass Azithromycin Distribution 
Background
To eliminate blinding trachoma, the World Health Organization emphasizes implementing the SAFE strategy, which includes annual mass drug administration (MDA) with azithromycin to the whole population of endemic districts. Prevalence surveys to assess impact at the district level are recommended after at least 3 years of intervention. The decision to stop MDA is based on a prevalence of trachomatous inflammation follicular (TF) among children aged 1–9 years below 5% at the sub-district level, as determined by an additional round of surveys limited within districts where TF prevalence is below 10%. We conducted impact surveys powered to estimate prevalence simultaneously at the sub-district and district in two zones of Amhara, Ethiopia to determine whether MDA could be stopped.
Methodology
Seventy-two separate population-based, sub-district surveys were conducted in 25 districts. In each survey all residents from 10 randomly selected clusters were screened for clinical signs of trachoma. Data were weighted according to selection probabilities and adjusted for correlation due to clustering.
Principal Findings
Overall, 89,735 residents were registered from 21,327 households of whom 72,452 people (80.7%) were examined. The prevalence of TF in children aged 1–9 years was below 5% in six sub-districts and two districts. Sub-district level prevalence of TF in children aged 1–9 years ranged from 0.9–76.9% and district-level from 0.9–67.0%. In only one district was the prevalence of trichiasis below 0.1%.
Conclusions/Significance
The experience from these zones in Ethiopia demonstrates that impact assessments designed to give a prevalence estimate of TF at sub-district level are possible, although the scale of the work was challenging. Given the assessed district-level prevalence of TF, sub-district-level surveys would have been warranted in only five districts. Interpretation was not as simple as stopping MDA in sub-districts below 5% given programmatic challenges of exempting sub-districts from a highly regarded program and the proximity of hyper-endemic sub-districts.
Author Summary
Trachoma, the leading cause of preventable blindness, is targeted for “elimination as a public health problem” by the year 2020. National programs are implementing the recommended strategy of surgery, antibiotics, facial cleanliness, and environmental improvements (SAFE) to meet this target. Many programs are currently facing the decision of when to scale down interventions, particularly mass drug administration (MDA) of azithromycin. We implemented large population-based surveys in two different zones of the Amhara National Regional State of Ethiopia. Rather than conducting an impact assessment first at the district level, followed by additional sub-district-level surveys, we took a novel approach to measure the prevalence of trachoma at sub-district level to be able to make an immediate decision of whether to stop MDA. Over 72,000 people in 714 communities in 72 sub-districts were examined for clinical signs of trachoma. We identified only six sub-districts that met criteria for being able to stop MDA. Our work demonstrates that determining the prevalence of trachoma at sub-district level is feasible but requires significant resources. In this hyper-endemic setting, sub-district-level surveys were not needed in the majority of districts. Overall, the clinical data suggest some decline in trachoma within these areas since the SAFE strategy was implemented.
doi:10.1371/journal.pntd.0002732
PMCID: PMC3953063  PMID: 24625539
11.  EXOSC3 mutations in pontocerebellar hypoplasia type 1: novel mutations and genotype-phenotype correlations 
Background
Pontocerebellar hypoplasia (PCH) represents a group of neurodegenerative disorders with prenatal onset. Eight subtypes have been described thus far (PCH1-8) based on clinical and genetic features. Common characteristics include hypoplasia and atrophy of the cerebellum, variable pontine atrophy, and severe mental and motor impairments. PCH1 is distinctly characterized by the combination with degeneration of spinal motor neurons. Recently, mutations in the exosome component 3 gene (EXOSC3) have been identified in approximately half of the patients with PCH subtype 1.
Methods
We selected a cohort of 99 PCH patients (90 families) tested negative for mutations in the TSEN genes, RARS2, VRK1 and CASK. Patients in this cohort were referred with a tentative diagnose PCH type 1, 2, 4, 7 or unclassified PCH. Genetic analysis of the EXOSC3 gene was performed using Sanger sequencing. Clinical data, MR images and autopsy reports of patients positive for EXOSC3 mutations were analyzed.
Results
EXOSC3 mutations were found in twelve families with PCH subtype 1, and were not found in patients with other PCH subtypes. Identified mutations included a large deletion, nonsense and missense mutations. Examination of clinical data reveals a prolonged disease course in patients with a homozygous p.D132A mutation. MRI shows variable pontine hypoplasia in EXOSC3 mediated PCH, where the pons is largely preserved in patients with a homozygous p.D132A mutation, but attenuated in patients with other mutations. Additionally, bilateral cerebellar cysts were found in patients compound heterozygous for a p.D132A mutation and a nonsense allele.
Conclusions
EXOSC3 mediated PCH shows clear genotype-phenotype correlations. A homozygous p.D132A mutation leads to PCH with possible survival into early puberty, and preservation of the pons. Compound heterozygosity for a p.D132A mutation and a nonsense or p.Y109N allele, a homozygous p.G31A mutation or a p.G135E mutation causes a more rapidly progressive course leading to death in infancy and attenuation of the ventral pons.
Our findings imply a clear correlation between genetic mutation and clinical outcome in EXOSC3 mediated PCH, including variable involvement of the pons.
doi:10.1186/1750-1172-9-23
PMCID: PMC3928094  PMID: 24524299
Pontocerebellar hypoplasia; Neurodegeneration; EXOSC3 gene; Genotype-phenotype correlations
12.  Loss of function germline mutations in RAD51D in women with ovarian carcinoma 
Gynecologic oncology  2012;127(3):552-555.
Objective
RAD51D, a gene in the Fanconi Anemia-BRCA homologous recombination pathway, has recently been shown to harbor germline mutations responsible for ovarian carcinoma in multiply affected families. We aimed to extend these results to ovarian carcinoma in the general population.
Methods
We sequenced RAD51D in germline DNA from 360 individuals with primary ovarian, peritoneal or fallopian tube carcinoma who were not selected for age of cancer onset or family history. We also sequenced RAD51D in 459 probands from 226 high risk breast cancer families who were wild type for 21 breast and ovarian cancer genes.
Results
Of 360 cases, three (0.8%) carried loss-of-function mutations in RAD51D. All three subjects had ovarian carcinoma; one was also diagnosed with a synchronous endometrial carcinoma. Only one of the three subjects had a family history of breast or ovarian cancer. Combined with previous data for this series, 23.9% of women with unselected ovarian, fallopian tube, or peritoneal carcinoma carried a germline loss-of-function mutation in any of 13 tumor suppressor genes. Among the 449 women and 10 men with familial breast cancer, none carried a loss of function mutation in RAD51D.
Conclusions
These data support the previous observation that loss-of-function mutations in RAD51D predispose to ovarian carcinoma but not to breast carcinoma. We conclude that inherited ovarian cancer is highly heterogeneous genetically, and that approximately one in four ovarian carcinoma patients carry a germline mutation in a known tumor suppressor gene that confers high risk.
doi:10.1016/j.ygyno.2012.09.009
PMCID: PMC3905744  PMID: 22986143
13.  Treatable childhood neuronopathy caused by mutations in riboflavin transporter RFVT2 
Brain  2013;137(1):44-56.
Childhood onset motor neuron diseases or neuronopathies are a clinically heterogeneous group of disorders. A particularly severe subgroup first described in 1894, and subsequently called Brown-Vialetto-Van Laere syndrome, is characterized by progressive pontobulbar palsy, sensorineural hearing loss and respiratory insufficiency. There has been no treatment for this progressive neurodegenerative disorder, which leads to respiratory failure and usually death during childhood. We recently reported the identification of SLC52A2, encoding riboflavin transporter RFVT2, as a new causative gene for Brown-Vialetto-Van Laere syndrome. We used both exome and Sanger sequencing to identify SLC52A2 mutations in patients presenting with cranial neuropathies and sensorimotor neuropathy with or without respiratory insufficiency. We undertook clinical, neurophysiological and biochemical characterization of patients with mutations in SLC52A2, functionally analysed the most prevalent mutations and initiated a regimen of high-dose oral riboflavin. We identified 18 patients from 13 families with compound heterozygous or homozygous mutations in SLC52A2. Affected individuals share a core phenotype of rapidly progressive axonal sensorimotor neuropathy (manifesting with sensory ataxia, severe weakness of the upper limbs and axial muscles with distinctly preserved strength of the lower limbs), hearing loss, optic atrophy and respiratory insufficiency. We demonstrate that SLC52A2 mutations cause reduced riboflavin uptake and reduced riboflavin transporter protein expression, and we report the response to high-dose oral riboflavin therapy in patients with SLC52A2 mutations, including significant and sustained clinical and biochemical improvements in two patients and preliminary clinical response data in 13 patients with associated biochemical improvements in 10 patients. The clinical and biochemical responses of this SLC52A2-specific cohort suggest that riboflavin supplementation can ameliorate the progression of this neurodegenerative condition, particularly when initiated soon after the onset of symptoms.
doi:10.1093/brain/awt315
PMCID: PMC3891447  PMID: 24253200
childhood neuronopathy; Brown-Vialetto-Van Laere syndrome; riboflavin therapy; RFVT2; SLC52A2
14.  Response to DNA damage of CHEK2 missense mutations in familial breast cancer 
Human Molecular Genetics  2012;21(12):2738-2744.
Comprehensive sequencing of tumor suppressor genes to evaluate inherited predisposition to cancer yields many individually rare missense alleles of unknown functional and clinical consequence. To address this problem for CHEK2 missense alleles, we developed a yeast-based assay to assess in vivo CHEK2-mediated response to DNA damage. Of 25 germline CHEK2 missense alleles detected in familial breast cancer patients, 12 alleles had complete loss of DNA damage response, 8 had partial loss and 5 exhibited a DNA damage response equivalent to that mediated by wild-type CHEK2. Variants exhibiting reduced response to DNA damage were found in all domains of the CHEK2 protein. Assay results were in agreement with epidemiologic assessments of breast cancer risk for those variants sufficiently common for case–control studies to have been undertaken. Assay results were largely concordant with consensus predictions of in silico tools, particularly for damaging alleles in the kinase domain. However, of the 25 variants, 6 were not consistently classifiable by in silico tools. An in vivo assay of cellular response to DNA damage by mutant CHEK2 alleles may complement and extend epidemiologic and genetic assessment of their clinical consequences.
doi:10.1093/hmg/dds101
PMCID: PMC3363333  PMID: 22419737
15.  A truncating mutation in GPSM2 is associated with recessive nonsyndromic hearing loss 
Clinical genetics  2011;81(3):289-293.
Hereditary deafness is a genetically heterogeneous phenotype for which more than 100 genomic loci have been identified thus far. By analysis of a consanguineous Palestinian family, GPSM2 was recently discovered to be the cause of autosomal recessive nonsyndromic hearing loss DFNB82. Here, we report a second truncating mutation, GPSM2 p.Q562X, identified via autozygosity mapping in a consanguineous Turkish family. This report provides evidence for allelic heterogeneity of GPSM2 and confirms its causative role for nonsyndromic deafness.
doi:10.1111/j.1399-0004.2011.01654.x
PMCID: PMC3657750  PMID: 21348867
Autosomal recessive; deafness; GPSM2; hearing loss; homozygosity; genome-wide SNP genotyping
16.  De novo mutations in ATP1A3 cause alternating hemiplegia of childhood 
Heinzen, Erin L. | Swoboda, Kathryn J. | Hitomi, Yuki | Gurrieri, Fiorella | Nicole, Sophie | de Vries, Boukje | Tiziano, F. Danilo | Fontaine, Bertrand | Walley, Nicole M. | Heavin, Sinéad | Panagiotakaki, Eleni | Fiori, Stefania | Abiusi, Emanuela | Di Pietro, Lorena | Sweney, Matthew T. | Newcomb, Tara M. | Viollet, Louis | Huff, Chad | Jorde, Lynn B. | Reyna, Sandra P. | Murphy, Kelley J. | Shianna, Kevin V. | Gumbs, Curtis E. | Little, Latasha | Silver, Kenneth | Ptác̆ek, Louis J. | Haan, Joost | Ferrari, Michel D. | Bye, Ann M. | Herkes, Geoffrey K. | Whitelaw, Charlotte M. | Webb, David | Lynch, Bryan J. | Uldall, Peter | King, Mary D. | Scheffer, Ingrid E. | Neri, Giovanni | Arzimanoglou, Alexis | van den Maagdenberg, Arn M.J.M. | Sisodiya, Sanjay M. | Mikati, Mohamad A. | Goldstein, David B. | Nicole, Sophie | Gurrieri, Fiorella | Neri, Giovanni | de Vries, Boukje | Koelewijn, Stephany | Kamphorst, Jessica | Geilenkirchen, Marije | Pelzer, Nadine | Laan, Laura | Haan, Joost | Ferrari, Michel | van den Maagdenberg, Arn | Zucca, Claudio | Bassi, Maria Teresa | Franchini, Filippo | Vavassori, Rosaria | Giannotta, Melania | Gobbi, Giuseppe | Granata, Tiziana | Nardocci, Nardo | De Grandis, Elisa | Veneselli, Edvige | Stagnaro, Michela | Gurrieri, Fiorella | Neri, Giovanni | Vigevano, Federico | Panagiotakaki, Eleni | Oechsler, Claudia | Arzimanoglou, Alexis | Nicole, Sophie | Giannotta, Melania | Gobbi, Giuseppe | Ninan, Miriam | Neville, Brian | Ebinger, Friedrich | Fons, Carmen | Campistol, Jaume | Kemlink, David | Nevsimalova, Sona | Laan, Laura | Peeters-Scholte, Cacha | van den Maagdenberg, Arn | Casaer, Paul | Casari, Giorgio | Sange, Guenter | Spiel, Georg | Boneschi, Filippo Martinelli | Zucca, Claudio | Bassi, Maria Teresa | Schyns, Tsveta | Crawley, Francis | Poncelin, Dominique | Vavassori, Rosaria
Nature genetics  2012;44(9):1030-1034.
Alternating hemiplegia of childhood (AHC) is a rare, severe neurodevelopmental syndrome characterized by recurrent hemiplegic episodes and distinct neurologic manifestations. AHC is usually a sporadic disorder with unknown etiology. Using exome sequencing of seven patients with AHC, and their unaffected parents, we identified de novo nonsynonymous mutations in ATP1A3 in all seven AHC patients. Subsequent sequence analysis of ATP1A3 in 98 additional patients revealed that 78% of AHC cases have a likely causal ATP1A3 mutation, including one inherited mutation in a familial case of AHC. Remarkably, six ATP1A3 mutations explain the majority of patients, including one observed in 36 patients. Unlike ATP1A3 mutations that cause rapid-onset-dystonia-parkinsonism, AHC-causing mutations revealed consistent reductions in ATPase activity without effects on protein expression. This work identifies de novo ATP1A3 mutations as the primary cause of AHC, and offers insight into disease pathophysiology by expanding the spectrum of phenotypes associated with mutations in this gene.
doi:10.1038/ng.2358
PMCID: PMC3442240  PMID: 22842232
17.  Host genotype-specific therapies can optimize the inflammatory response to mycobacterial infections 
Cell  2012;148(3):434-446.
Summary
Susceptibility to tuberculosis is historically ascribed to an inadequate immune response that fails to control infecting mycobacteria. In zebrafish, we find that susceptibility to Mycobacterium marinum can result from either inadequate or excessive acute inflammation. Modulation of the leukotriene A4 hydrolase (LTA4H) locus, which controls the balance of pro- and anti-inflammatory eicosanoids, reveals two distinct molecular routes to mycobacterial susceptibility converging on dysregulated TNF levels: inadequate inflammation caused by excess lipoxins and hyperinflammation driven by excess leukotriene B4. We identify therapies that specifically target each of these extremes. In humans, we identify a single nucleotide polymorphism in the LTA4H promoter that regulates its transcriptional activity. In tuberculous meningitis, the polymorphism is associated with inflammatory cell recruitment, patient survival and response to adjunctive anti-inflammatory therapy. Together, our findings suggest that host-directed therapies tailored to patient LTA4H genotypes may counter detrimental effects of either extreme of inflammation.
doi:10.1016/j.cell.2011.12.023
PMCID: PMC3433720  PMID: 22304914
18.  Effect of Dissemination of Evidence in Reducing Injuries from Falls 
The New England journal of medicine  2008;359(3):252-261.
Background
Falling is a common and morbid condition among elderly persons. Effective strategies to prevent falls have been identified but are underutilized.
Methods
Using a nonrandomized design, we compared rates of injuries from falls in a region of Connecticut where clinicians had been exposed to interventions to change clinical practice (intervention region) and in a region where clinicians had not been exposed to such interventions (usual-care region). The interventions encouraged primary care clinicians and staff members involved in home care, outpatient rehabilitation, and senior centers to adopt effective risk assessments and strategies for the prevention of falls (e.g., medication reduction and balance and gait training). The outcomes were rates of serious fall-related injuries (hip and other fractures, head injuries, and joint dislocations) and fall-related use of medical services per 1000 person-years among persons who were 70 years of age or older. The interventions occurred from 2001 to 2004, and the evaluations took place from 2004 to 2006.
Results
Before the interventions, the adjusted rates of serious fall-related injuries (per 1000 person-years) were 31.2 in the usual-care region and 31.9 in the intervention region. During the evaluation period, the adjusted rates were 31.4 and 28.6, respectively (adjusted rate ratio, 0.91; 95% Bayesian credibility interval, 0.88 to 0.94). Between the preintervention period and the evaluation period, the rate of fall-related use of medical services increased from 68.1 to 83.3 per 1000 person-years in the usual-care region and from 70.7 to 74.2 in the intervention region (adjusted rate ratio, 0.89; 95% credibility interval, 0.86 to 0.92). The percentages of clinicians who received intervention visits ranged from 62% (131 of 212 primary care offices) to 100% (26 of 26 home care agencies).
Conclusions
Dissemination of evidence about fall prevention, coupled with interventions to change clinical practice, may reduce fall-related injuries in elderly persons.
doi:10.1056/NEJMoa0801748
PMCID: PMC3472807  PMID: 18635430
19.  Inherited mutation of the luteinizing hormone/choriogonadotropin receptor (LHCGR) in empty follicle syndrome 
Fertility and sterility  2011;96(2):e125-e130.
Objective
To test by genomic analysis whether empty follicle syndrome (EFS) in a family with two affected sisters has a genetic basis.
Design
Whole-exome sequencing in the context of clinical genetics.
Setting
University hospital.
Patient(s)
Two women (36 and 32 years old at the time of the study) with EFS.
Intervention(s)
Genetic counseling based on autosomal recessive inheritance.
Main Outcome Measure(s)
Discovery of a mutation in the LH/choriogonadotropin receptor (LHCGR) as the cause of EFS.
Result(s)
A novel missense mutation in LHCGR, p.N400S, was homozygous in sisters with EFS and/or infertility, but not in their unaffected siblings or parents. The mutation was not present in 500 ancestry-matched control subjects. Asparagine at residue 400 is highly conserved and its substitution by serine predicted to alter critical interactions that stabilize LHCGR.
Conclusion(s)
We describe a genetic basis for EFS and provide strong evidence for the existence of genuine EFS in some patients. A mutation impairing the function of LHCGR explains the lack of response of these patients to repeated administration of β-hCG.
doi:10.1016/j.fertnstert.2011.05.057
PMCID: PMC3143235  PMID: 21683950
Empty follicle syndrome; luteinizing hormone/choriogonadotropin receptor; infertility; next-generation sequencing
20.  Reduced transcript expression of genes affected by inherited and de novo CNVs in autism 
Individuals with autism are more likely to carry rare inherited and de novo copy number variants (CNVs). However, further research is needed to establish which CNVs are causal and the mechanisms by which these CNVs influence autism. We examined genomic DNA of children with autism (N=41) and healthy controls (N=367) for rare CNVs using a high-resolution array comparative genomic hybridization platform. We show that individuals with autism are more likely to harbor rare CNVs as small as ∼10 kb, a threshold not previously detectable, and that CNVs in cases disproportionately affect genes involved in transcription, nervous system development, and receptor activity. We also show that a subset of genes that have known or suspected allele-specific or imprinting effects and are within rare-case CNVs may undergo loss of transcript expression. In particular, expression of CNTNAP2 and ZNF214 are decreased in probands compared with their unaffected transmitting parents. Furthermore, expression of PRODH and ARID1B, two genes affected by de novo CNVs, are decreased in probands compared with controls. These results suggest that for some genes affected by CNVs in autism, reduced transcript expression may be a mechanism of pathogenesis during neurodevelopment.
doi:10.1038/ejhg.2011.24
PMCID: PMC3110052  PMID: 21448237
autism; CNV; aCGH; expression; deletion; duplication
21.  Duplications of the Neuropeptide Receptor VIPR2 Confer Significant Risk for Schizophrenia 
Nature  2011;471(7339):499-503.
Rare copy number variants (CNVs) play a prominent role in the etiology of schizophrenia and other neuropsychiatric disorders1. Substantial risk for schizophrenia is conferred by large (>500 kb) CNVs at several loci, including microdeletions at 1q21.1 2, 3q29 3, 15q13.3 2 and 22q11.2 4 and microduplication at 16p11.2 5. However, these CNVs collectively account for a small fraction (2-4%) of cases, and the relevant genes and neurobiological mechanisms are not well understood. Here we performed a large two-stage genome-wide scan of rare CNVs and report the significant association of copy number gains at chromosome 7q36.3 with schizophrenia (P= 4.0×10-5, OR = 16.14 [3.06, ∞]). Microduplications with variable breakpoints occurred within a 362 kb region and were detected in 29 of 8,290 (0.35%) patients versus two of 7,431 (0.03%) controls in the combined sample (p-value= 5.7×10-7, odds ratio (OR) = 14.1 [3.5, 123.9]). All duplications overlapped or were located within 89 kb upstream of the vasoactive intestinal peptide receptor VIPR2. VIPR2 transcription and cyclic-AMP signaling were significantly increased in cultured lymphocytes from patients with microduplications of 7q36.3. These findings implicate altered VIP signaling in the pathogenesis of schizophrenia and suggest VIPR2 as a potential target for the development of novel antipsychotic drugs.
doi:10.1038/nature09884
PMCID: PMC3351382  PMID: 21346763
22.  CONTRIBUTION TO FAMILIAL BREAST CANCER OF INHERITED MUTATIONS IN THE BRCA2-INTERACTING PROTEIN PALB2 
Cancer research  2011;71(6):2222-2229.
Inherited mutations in the BRCA2-interacting protein PALB2 are known to be associated with increased risks of breast cancer. In order to evaluate the contribution of PALB2 to familial breast cancer in the United States, we sequenced the coding sequences and flanking regulatory regions of the gene from constitutional genomic DNA of 1144 familial breast cancer patients with wildtype sequences at BRCA1 and BRCA2. Overall, 3.4% (33/972) of patients not selected by ancestry and 0% (0/172) of patients specifically of Ashkenazi Jewish ancestry were heterozygous for a nonsense, frameshift, or frameshift-associated splice mutation in PALB2. Mutations were detected in both male and female breast cancer patients. All mutations were individually rare: the 33 heterozygotes harbored 13 different mutations, 5 previously reported and 8 novel. PALB2 heterozygotes were 4-fold more likely to have a male relative with breast cancer (P=0.0003) and 6-fold more likely to have a relative with pancreatic cancer (P=0.002), and 1.3-fold more likely to have a relative with ovarian cancer (P=0.18). Compared to their female relatives without mutations, increased risk of breast cancer for female PALB2 heterozygotes was 2.3-fold (95%CI [1.5–4.2]) by age 55 and 3.4-fold (95%CI [2.4–5.9]) by age 85. Loss of the wildtype PALB2 allele was observed in laser dissected tumor specimens from heterozygous patients. Given this mutation prevalence and risk, consideration might be given to clinical testing of PALB2 by complete genomic sequencing for familial breast cancer patients with wildtype sequences at BRCA1 and BRCA2.
doi:10.1158/0008-5472.CAN-10-3958
PMCID: PMC3059378  PMID: 21285249
23.  A Genomewide Screen for Suppressors of Alu-Mediated Rearrangements Reveals a Role for PIF1 
PLoS ONE  2012;7(2):e30748.
Alu-mediated rearrangement of tumor suppressor genes occurs frequently during carcinogenesis. In breast cancer, this mechanism contributes to loss of the wild-type BRCA1 allele in inherited disease and to loss of heterozygosity in sporadic cancer. To identify genes required for suppression of Alu-mediated recombination we performed a genomewide screen of a collection of 4672 yeast gene deletion mutants using a direct repeat recombination assay. The primary screen and subsequent analysis identified 12 candidate genes including TSA, ELG1, and RRM3, which are known to play a significant role in maintaining genomic stability. Genetic analysis of the corresponding human homologs was performed in sporadic breast tumors and in inherited BRCA1-associated carcinomas. Sequencing of these genes in high risk breast cancer families revealed a potential role for the helicase PIF1 in cancer predisposition. PIF1 variant L319P was identified in three breast cancer families; importantly, this variant, which is predicted to be functionally damaging, was not identified in a large series of controls nor has it been reported in either dbSNP or the 1000 Genomes Project. In Schizosaccharomyces pombe, Pfh1 is required to maintain both mitochondrial and nuclear genomic integrity. Functional studies in yeast of human PIF1 L319P revealed that this variant cannot complement the essential functions of Pfh1 in either the nucleus or mitochondria. Our results provide a global view of nonessential genes involved in suppressing Alu-mediated recombination and implicate variation in PIF1 in breast cancer predisposition.
doi:10.1371/journal.pone.0030748
PMCID: PMC3276492  PMID: 22347400
24.  Nanos1 functions as a translational repressor in the Xenopus germline 
Mechanisms of development  2010;128(1-2):153-163.
Nanos family members have been shown to act as translational repressors in the Drosophila and Caenorhabditis elegans germline, but direct evidence is missing for a similar function in vertebrates. Using a tethered function assay, we show that Xenopus Nanos1 is a translational repressor and that association with the RNA is required for this repression. We identified a 14 amino acid region within the N-terminal domain of Nanos1 that is conserved in organisms as diverse as sponge and Human. The region is found in all vertebrates but notably lacking in Drosophila and C. elegans. Deletion and substitution analysis revealed that this conserved region was required for Nanos1 repressive activity. Consistent with this observation, deletion of this region was sufficient to prevent abnormal development that results from ectopic expression of Nanos1 in oocytes. Although Nanos1 can repress capped and polyadenylated RNAs, Nanos1 mediated repression did not require the targeted RNA to have a cap or to be polyadenylated. These results suggest that Nanos1 is capable of repressing translation by several different mechanisms. We found that Nanos1, like Drosophila Nanos, associates with cyclin B1 RNA in vivo indicating that some Nanos targets may be evolutionarily conserved. Nanos1 protein was detected and thus available to repress mRNAs while PGCs were in the endoderm, but was not observed in PGCs after this stage.
doi:10.1016/j.mod.2010.12.001
PMCID: PMC3065925  PMID: 21195170
Xenopus; Nanos1/Xcat2; germline determination; translational repression
25.  Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in middle eastern families 
Genome Biology  2011;12(9):R89.
Background
Identification of genes responsible for medically important traits is a major challenge in human genetics. Due to the genetic heterogeneity of hearing loss, targeted DNA capture and massively parallel sequencing are ideal tools to address this challenge. Our subjects for genome analysis are Israeli Jewish and Palestinian Arab families with hearing loss that varies in mode of inheritance and severity.
Results
A custom 1.46 MB design of cRNA oligonucleotides was constructed containing 246 genes responsible for either human or mouse deafness. Paired-end libraries were prepared from 11 probands and bar-coded multiplexed samples were sequenced to high depth of coverage. Rare single base pair and indel variants were identified by filtering sequence reads against polymorphisms in dbSNP132 and the 1000 Genomes Project. We identified deleterious mutations in CDH23, MYO15A, TECTA, TMC1, and WFS1. Critical mutations of the probands co-segregated with hearing loss. Screening of additional families in a relevant population was performed. TMC1 p.S647P proved to be a founder allele, contributing to 34% of genetic hearing loss in the Moroccan Jewish population.
Conclusions
Critical mutations were identified in 6 of the 11 original probands and their families, leading to the identification of causative alleles in 20 additional probands and their families. The integration of genomic analysis into early clinical diagnosis of hearing loss will enable prediction of related phenotypes and enhance rehabilitation. Characterization of the proteins encoded by these genes will enable an understanding of the biological mechanisms involved in hearing loss.
doi:10.1186/gb-2011-12-9-r89
PMCID: PMC3308052  PMID: 21917145

Results 1-25 (58)