Bio

Clinical Focus


  • Cleft Palate
  • Clinical Genetics
  • Cleft Lip
  • Craniofacial Abnormalities
  • Developmental Disorders
  • Craniosynostosis
  • Autism
  • Cardiovascular Genetics

Academic Appointments


Administrative Appointments


  • Director, Stanford Medical Genetics Residency Program (2013 - Present)
  • Associate Director, Medical Genetics Residency Program (2008 - 2013)

Professional Education


  • Fellowship:Lucile Packard Children's Hospital (2008) CA
  • Board Certification: Clinical Genetics, American Board of Medical Genetics (2009)
  • Residency:Lucile Packard Children's Hospital (2006) CA
  • PhD, Stanford University, Genetics (2003)
  • Medical Education:Stanford School of Medicine (2003) CA

Research & Scholarship

Current Research and Scholarly Interests


I am interested in the genetics of autism spectrum and other developmental disorders. In collaboration with colleagues at Stanford, I am working to develop induced pluripotent stem cell (iPSC) models of genetic disorders associated with autism and developmental disability. I am also engaged in the application of new technologies for the diagnosis of genetic etiologies for developmental disorders.

Teaching

2013-14 Courses


Publications

Journal Articles


  • Clinical interpretation and implications of whole-genome sequencing. JAMA : the journal of the American Medical Association Dewey, F. E., Grove, M. E., Pan, C., Goldstein, B. A., Bernstein, J. A., Chaib, H., Merker, J. D., Goldfeder, R. L., Enns, G. M., David, S. P., Pakdaman, N., Ormond, K. E., Caleshu, C., Kingham, K., Klein, T. E., Whirl-Carrillo, M., Sakamoto, K., Wheeler, M. T., Butte, A. J., Ford, J. M., Boxer, L., Ioannidis, J. P., Yeung, A. C., Altman, R. B., Assimes, T. L., Snyder, M., Ashley, E. A., Quertermous, T. 2014; 311 (10): 1035-1045

    Abstract

    Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication.To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings.An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings.Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up.Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95% CI, 0.40-0.64), and reclassified 69% of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001).In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine.

    View details for DOI 10.1001/jama.2014.1717

    View details for PubMedID 24618965

  • Clinical whole-exome sequencing: are we there yet? Genetics in medicine : official journal of the American College of Medical Genetics Atwal, P. S., Brennan, M. L., Cox, R., Niaki, M., Platt, J., Homeyer, M., Kwan, A., Parkin, S., Schelley, S., Slattery, L., Wilnai, Y., Bernstein, J. A., Enns, G. M., Hudgins, L. 2014

    Abstract

    Background:Clinical laboratories began offering whole-exome sequencing in 2011 at a cost between $4,500 and $9,000. Reported detection rates for deleterious mutations range from 25 to 50%. Based on the experience of our clinical genetics service, actual success rates may be lower than estimated rates. We report results from our own experience along with a survey of clinical geneticists to ascertain (i) current success rates for causal gene detection in a clinical setting; (ii) if there are insurance authorization issues; and (iii) if turnaround times quoted by the clinical laboratories are accurate; we also gauge provider opinions toward clinical whole-exome sequencing.Methods:We reviewed our results and the results of a survey that was electronically distributed to 47 clinical genetics centers.Results:A total of 35 exome reports were available. If all positive results are collated, we observe a success rate of 22.8%. One result incorrectly identified a known benign variant as pathogenic. Some insurers covered all testing, whereas others denied any insurance coverage. Only three (23.1%) of our reports were available within the laboratory's quoted turnaround times. More than 50% of clinicians queried in our survey had not ordered whole-exome sequencing at the current time, many stating concerns regarding interpretation, insurance coverage, and cost.Conclusion:Clinical whole-exome sequencing has proven diagnostic utility; however, currently many clinicians have concerns regarding interpretation of results, insurance coverage, and cost.Genet Med advance online publication 13 February 2014Genetics in Medicine (2014); doi:10.1038/gim.2014.10.

    View details for DOI 10.1038/gim.2014.10

    View details for PubMedID 24525916

  • SHANK3 and IGF1 restore synaptic deficits in neurons from 22q13 deletion syndrome patients NATURE Shcheglovitov, A., Shcheglovitova, O., Yazawa, M., Portmann, T., Shu, R., Sebastiano, V., Krawisz, A., Froehlich, W., Bernstein, J. A., Hallmayer, J. F., Dolmetsch, R. E. 2013; 503 (7475): 267-?

    Abstract

    Phelan-McDermid syndrome (PMDS) is a complex neurodevelopmental disorder characterized by global developmental delay, severely impaired speech, intellectual disability, and an increased risk of autism spectrum disorders (ASDs). PMDS is caused by heterozygous deletions of chromosome 22q13.3. Among the genes in the deleted region is SHANK3, which encodes a protein in the postsynaptic density (PSD). Rare mutations in SHANK3 have been associated with idiopathic ASDs, non-syndromic intellectual disability, and schizophrenia. Although SHANK3 is considered to be the most likely candidate gene for the neurological abnormalities in PMDS patients, the cellular and molecular phenotypes associated with this syndrome in human neurons are unknown. We generated induced pluripotent stem (iPS) cells from individuals with PMDS and autism and used them to produce functional neurons. We show that PMDS neurons have reduced SHANK3 expression and major defects in excitatory, but not inhibitory, synaptic transmission. Excitatory synaptic transmission in PMDS neurons can be corrected by restoring SHANK3 expression or by treating neurons with insulin-like growth factor 1 (IGF1). IGF1 treatment promotes formation of mature excitatory synapses that lack SHANK3 but contain PSD95 and N-methyl-D-aspartate (NMDA) receptors with fast deactivation kinetics. Our findings provide direct evidence for a disruption in the ratio of cellular excitation and inhibition in PMDS neurons, and point to a molecular pathway that can be recruited to restore it.

    View details for DOI 10.1038/nature12618

    View details for Web of Science ID 000326894200052

    View details for PubMedID 24132240

  • ß-Galactosidosis in Patient with Intermediate GM1 and MBD Phenotype. JIMD reports Moore, T., Bernstein, J. A., Casson-Parkin, S., Cowan, T. M. 2013; 7: 77-79

    Abstract

    A 5-year-old girl with clinical and biochemical phenotypes encompassing both GM1-gangliosidosis (GM1) and Morquio B disease (MBD) is described. Mild generalized skeletal dysplasia and keratan sulfaturia were consistent with a diagnosis of MBD, while developmental delay and GM1-specific oligosacchariduria were consistent with GM1 gangliosidosis. No observable ?-galactosidase activity was detected in leukocytes, and two mutations, p.R201H (c.602G>A) and p.G311R (c.931G>A), were identified by gene sequencing. The R201H substitution has been previously reported in patients with both GM1 and MBD, and G311R is a novel mutation. Our patient represents a further example of the clinical heterogeneity that can result from mutations at the ?-galactosidase locus.

    View details for DOI 10.1007/8904_2012_145

    View details for PubMedID 23430499

  • Underutilization of Genetics Services for Autism: The Importance of Parental Awareness and Provider Recommendation JOURNAL OF GENETIC COUNSELING Vande Wydeven, K., Kwan, A., Hardan, A. Y., Bernstein, J. A. 2012; 21 (6): 803-813

    Abstract

    Reasons for the underutilization of genetics services by families of children with autism spectrum disorders (ASD) are not well understood. We report the identification of factors associated with this underuse. Survey-based study of parents and/or guardians of children with ASD. One hundred fifty-five families completed the questionnaire. Thirty-one of 155 (20%) children had seen a genetics professional. Forty-nine of 154 (32%) children had undergone genetic testing. Parents whose child saw a genetics professional were more likely to 1) Have a primary provider refer for or suggest a genetics evaluation 2) Have asked for a referral, and/or 3) Know another person with a genetic cause of ASD. amilies of children with ASD who have not received genetics services are less aware of their availability and utility. They are also less likely to have their provider recommend a clinical genetics evaluation. Efforts should be taken to increase awareness of both health providers and parents regarding the usefulness of genetics services for ASD.

    View details for DOI 10.1007/s10897-012-9494-x

    View details for Web of Science ID 000311509200011

    View details for PubMedID 22415587

  • Spectrum of Mutations in the Renin-Angiotensin System Genes in Autosomal Recessive Renal Tubular Dysgenesis HUMAN MUTATION Gribouval, O., Moriniere, V., Pawtowski, A., Arrondel, C., Sallinen, S., Saloranta, C., Clericuzio, C., Viot, G., Tantau, J., Blesson, S., Cloarec, S., Machet, M. C., Chitayat, D., Thauvin, C., Laurent, N., Sampson, J. R., Bernstein, J. A., Clemenson, A., Prieur, F., Daniel, L., Levy-Mozziconacci, A., Lachlan, K., Alessandri, J. L., Cartault, F., Riviere, J. P., Picard, N., Baumann, C., Delezoide, A. L., Belar Ortega, M., Chassaing, N., Labrune, P., Yu, S., Firth, H., Wellesley, D., Bitzan, M., Alfares, A., Braverman, N., Krogh, L., Tolmie, J., Gaspar, H., Doray, B., Majore, S., Bonneau, D., Triau, S., Loirat, C., David, A., Bartholdi, D., Peleg, A., Brackman, D., Stone, R., DeBerardinis, R., Corvol, P., Michaud, A., Antignac, C., Gubler, M. C. 2012; 33 (2): 316-326

    Abstract

    Autosomal recessive renal tubular dysgenesis (RTD) is a severe disorder of renal tubular development characterized by early onset and persistent fetal anuria leading to oligohydramnios and the Potter sequence, associated with skull ossification defects. Early death occurs in most cases from anuria, pulmonary hypoplasia, and refractory arterial hypotension. The disease is linked to mutations in the genes encoding several components of the renin-angiotensin system (RAS): AGT (angiotensinogen), REN (renin), ACE (angiotensin-converting enzyme), and AGTR1 (angiotensin II receptor type 1). Here, we review the series of 54 distinct mutations identified in 48 unrelated families. Most of them are novel and ACE mutations are the most frequent, observed in two-thirds of families (64.6%). The severity of the clinical course was similar whatever the mutated gene, which underlines the importance of a functional RAS in the maintenance of blood pressure and renal blood flow during the life of a human fetus. Renal hypoperfusion, whether genetic or secondary to a variety of diseases, precludes the normal development/ differentiation of proximal tubules. The identification of the disease on the basis of precise clinical and histological analyses and the characterization of the genetic defects allow genetic counseling and early prenatal diagnosis.

    View details for DOI 10.1002/humu.21661

    View details for Web of Science ID 000300705600004

    View details for PubMedID 22095942

  • Analysis of the Alternative Splicing of an FGFR2 Transcript Due to a Novel 5 ' Splice Site Mutation (1084+1G > A): Case Report CLEFT PALATE-CRANIOFACIAL JOURNAL Traynis, I., Bernstein, J. A., Gardner, P., Schrijver, I. 2012; 49 (1): 104-108

    Abstract

    Craniosynostosis is characterized by premature fusion of one or more cranial sutures and is associated with mutations in fibroblast growth factor receptor (FGFR) genes. Here we describe a novel mutation (1084+1G>A) in the FGFR2 gene of a patient with isolated bicoronal synostosis. We detected two isoforms that result from the mutation and are characterized, respectively, by exon skipping and the use of a cryptic splice site. Interestingly, the alternatively spliced forms of FGFR2 appear to induce fusion of the cranial sutures suggesting that the mutation acts via a gain-of-function mechanism rather than a loss of protein functionality.

    View details for DOI 10.1597/10-217

    View details for Web of Science ID 000300352600014

    View details for PubMedID 21524234

  • Rapid Implementation of Inpatient Electronic Physician Documentation at an Academic Hospital APPLIED CLINICAL INFORMATICS Hahn, J. S., Bernstein, J. A., MCKENZIE, R. B., King, B. J., Longhurst, C. A. 2012; 3 (2): 175-185

    Abstract

    Electronic physician documentation is an essential element of a complete electronic medical record (EMR). At Lucile Packard Children's Hospital, a teaching hospital affiliated with Stanford University, we implemented an inpatient electronic documentation system for physicians over a 12-month period. Using an EMR-based free-text editor coupled with automated import of system data elements, we were able to achieve voluntary, widespread adoption of the electronic documentation process. When given the choice between electronic versus dictated report creation, the vast majority of users preferred the electronic method. In addition to increasing the legibility and accessibility of clinical notes, we also decreased the volume of dictated notes and scanning of handwritten notes, which provides the opportunity for cost savings to the institution.

    View details for DOI 10.4338/ACI-2012-02-CR-0003

    View details for Web of Science ID 000317183500003

    View details for PubMedID 23620718

  • Newborn with prenatally diagnosed choroidal fissure cyst and panhypopituitarism and review of the literature. AJP reports Chitkara, R., Rajani, A., Bernstein, J., Shah, S., Hahn, J. S., Barnes, P., Hintz, S. R. 2011; 1 (2): 111-114

    Abstract

    Little has been reported on fetal diagnosis of choroidal fissure cysts and prediction of the clinical complications that can result. We describe the case of a near-term male infant with prenatally diagnosed choroidal fissure cyst and bilateral clubfeet. His prolonged course in the neonatal intensive care nursery was marked by severe panhypopituitarism, late-onset diabetes insipidus, placement of a cystoperitoneal shunt, and episodes of sepsis. Postnatal genetic evaluation also revealed an interstitial deletion involving most of band 10q26.12 and the proximal half of band 10q26.13. The patient had multiple readmissions for medical and surgical indications and died at 6 months of age. This case represents the severe end of the spectrum of medical complications for children with choroidal fissure cysts. It highlights not only the importance of comprehensive evaluation and multidisciplinary management and counseling in such cases, but also the need for heightened vigilance in these patients.

    View details for DOI 10.1055/s-0031-1293512

    View details for PubMedID 23705098

  • Using iPSC-derived neurons to uncover cellular phenotypes associated with Timothy syndrome NATURE MEDICINE Pasca, S. P., Portmann, T., Voineagu, I., Yazawa, M., Shcheglovitov, A., Pasca, A. M., Cord, B., Palmer, T. D., Chikahisa, S., Nishino, S., Bernstein, J. A., Hallmayer, J., Geschwind, D. H., Dolmetsch, R. E. 2011; 17 (12): 1657-U176

    Abstract

    Monogenic neurodevelopmental disorders provide key insights into the pathogenesis of disease and help us understand how specific genes control the development of the human brain. Timothy syndrome is caused by a missense mutation in the L-type calcium channel Ca(v)1.2 that is associated with developmental delay and autism. We generated cortical neuronal precursor cells and neurons from induced pluripotent stem cells derived from individuals with Timothy syndrome. Cells from these individuals have defects in calcium (Ca(2+)) signaling and activity-dependent gene expression. They also show abnormalities in differentiation, including decreased expression of genes that are expressed in lower cortical layers and in callosal projection neurons. In addition, neurons derived from individuals with Timothy syndrome show abnormal expression of tyrosine hydroxylase and increased production of norepinephrine and dopamine. This phenotype can be reversed by treatment with roscovitine, a cyclin-dependent kinase inhibitor and atypical L-type-channel blocker. These findings provide strong evidence that Ca(v)1.2 regulates the differentiation of cortical neurons in humans and offer new insights into the causes of autism in individuals with Timothy syndrome.

    View details for DOI 10.1038/nm.2576

    View details for Web of Science ID 000297978000039

    View details for PubMedID 22120178

  • Ectopia Lentis as the Presenting and Primary Feature in Marfan Syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Zadeh, N., Bernstein, J. A., Niemi, A. K., Dugan, S., Kwan, A., Liang, D., Hyland, J. C., Hoyme, H. E., Hudgins, L., Manning, M. A. 2011; 155A (11): 2661-2668

    Abstract

    Marfan syndrome (MFS) is a multisystem connective tissue disorder with primary involvement of the ocular, cardiovascular, and skeletal systems. We report on eight patients, all presenting initially with bilateral ectopia lentis (EL) during early childhood. These individuals did not have systemic manifestations of MFS, and did not fulfill the revised Ghent diagnostic criteria. However, all patients had demonstratable, disease-causing missense mutations in the FBN1 gene. Based on molecular results, cardiovascular imaging was recommended and led to the identification of mild aortic root changes in seven of the eight patients. The remaining patient had mitral valve prolapse with a normal appearing thoracic aorta. The findings presented in this paper validate the necessity of FBN1 gene testing in all individuals presenting with isolated EL. As we observed, these individuals are at increased risk of cardiovascular complications. Furthermore, we also noted that the majority of our patient cohort's mutations occurred in the 5' portion of the FBN1 gene, and were found to affect highly conserved cysteine residues, which may indicate a possible genotype-phenotype correlation. We conclude that in patients with isolated features of EL, FBN1 mutation analysis is necessary to aid in providing prompt diagnosis, and to identify patients at risk for potentially life-threatening complications. Additionally, knowledge of the type and location of an FBN1 mutation may be useful in providing further clinical correlation regarding phenotypic progression and appropriate medical management.

    View details for DOI 10.1002/ajmg.a.34245

    View details for Web of Science ID 000297199700009

    View details for PubMedID 21932315

  • Horseshoe Kidney and a Rare TSC2 Variant in Two Unrelated Individuals With Tuberous Sclerosis Complex AMERICAN JOURNAL OF MEDICAL GENETICS PART A Niemi, A., Northrup, H., Hudgins, L., Bernstein, J. A. 2011; 155A (10): 2534-2537

    Abstract

    Tuberous sclerosis complex (TSC) is an autosomal dominant multisystem disorder characterized by abnormalities involving the skin, brain, kidney (angiomyolipomas, cysts), and heart. Horseshoe kidney has not been considered to be a common renal manifestation of TSC but it has been previously reported in two patients with TSC. We report on two unrelated females with typical manifestations of TSC, horseshoe kidney, and an identical variant c.5138G>A in exon 39 (p.Arg1713His) of TSC2 gene. These cases provide evidence that horseshoe kidney is associated with TSC and add to the evidence for the pathogenicity of this variant. Furthermore, one of the patients also had a diaphragmatic hernia which has been reported twice in the medical literature in individuals with TSC. It is possible that a diaphragmatic hernia is another rare manifestation of TSC and that TSC should be included in the differential diagnosis of infants with a diaphragmatic hernia. Given that both a horseshoe kidney and a diaphragmatic hernia are findings that can be detected prenatally on an ultrasound examination, our findings may have implications for prenatal genetic counseling.

    View details for DOI 10.1002/ajmg.a.34197

    View details for Web of Science ID 000295326300032

    View details for PubMedID 21910228

  • Familial Cardiac Valvulopathy Due to Filamin A Mutation AMERICAN JOURNAL OF MEDICAL GENETICS PART A Bernstein, J. A., Bernstein, D., Hehr, U., Hudgins, L. 2011; 155A (9): 2236-2241

    Abstract

    We report on the clinical findings in siblings affected by the recently characterized X-linked form of hereditary cardiac valvular dystrophy or cardiac valve disease (OMIM 314400) due to mutations in the FLNA gene and review the literature on this condition. Although FLNA related cardiac valve disease is presumed to be a rare disorder, it is likely underdiagnosed. Several features of this condition may aid in its identification. FLNA related valvular disease can be recognized on the basis of its distinctive inheritance, early age of onset, and frequent multi-valve involvement.

    View details for DOI 10.1002/ajmg.a.34132

    View details for Web of Science ID 000294182500031

    View details for PubMedID 21815255

  • Using induced pluripotent stem cells to investigate cardiac phenotypes in Timothy syndrome NATURE Yazawa, M., Hsueh, B., Jia, X., Pasca, A. M., Bernstein, J. A., Hallmayer, J., Dolmetsch, R. E. 2011; 471 (7337): 230-U120

    Abstract

    Individuals with congenital or acquired prolongation of the QT interval, or long QT syndrome (LQTS), are at risk of life-threatening ventricular arrhythmia. LQTS is commonly genetic in origin but can also be caused or exacerbated by environmental factors. A missense mutation in the L-type calcium channel Ca(V)1.2 leads to LQTS in patients with Timothy syndrome. To explore the effect of the Timothy syndrome mutation on the electrical activity and contraction of human cardiomyocytes, we reprogrammed human skin cells from Timothy syndrome patients to generate induced pluripotent stem cells, and differentiated these cells into cardiomyocytes. Electrophysiological recording and calcium (Ca(2+)) imaging studies of these cells revealed irregular contraction, excess Ca(2+) influx, prolonged action potentials, irregular electrical activity and abnormal calcium transients in ventricular-like cells. We found that roscovitine, a compound that increases the voltage-dependent inactivation of Ca(V)1.2 (refs 6-8), restored the electrical and Ca(2+) signalling properties of cardiomyocytes from Timothy syndrome patients. This study provides new opportunities for studying the molecular and cellular mechanisms of cardiac arrhythmias in humans, and provides a robust assay for developing new drugs to treat these diseases.

    View details for DOI 10.1038/nature09855

    View details for Web of Science ID 000288170200040

    View details for PubMedID 21307850

  • Clues to an Early Diagnosis of Kallmann Syndrome AMERICAN JOURNAL OF MEDICAL GENETICS PART A Kaplan, J. D., Bernstein, J. A., Kwan, A., Hudgins, L. 2010; 152A (11): 2796-2801

    Abstract

    Kallmann syndrome (KS) is defined by the association of idiopathic hypogonadotropic hypogonadism and anosmia/hyposmia. Diagnosis is frequently delayed, however, because hypogonadotropic hypogonadism is usually not apparent until puberty and individuals with anosmia/hyposmia are often unaware of this sensory deficit. Mutations in at least six genes have been associated with KS; however, the sensitivity of molecular testing is only about 30% and, therefore, the diagnosis is largely based on clinical findings. We describe the findings in six individuals with KS, which demonstrate the utility of associated anomalies in making this diagnosis. Analysis of our case series and literature review suggests the consideration of KS for males with microphallus and/or cryptorchidism and for any patient with hearing loss, renal agenesis, and/or synkinesis. Conversely, patients with features of KS should have an audiology evaluation and a renal ultrasound.

    View details for DOI 10.1002/ajmg.a.33442

    View details for Web of Science ID 000284005700019

    View details for PubMedID 20949504

  • Two-Tier Approach to the Newborn Screening of Methylenetetrahydrofolate Reductase Deficiency and Other Remethylation Disorders with Tandem Mass Spectrometry JOURNAL OF PEDIATRICS Tortorelli, S., Turgeon, C. T., Lim, J. S., Baumgart, S., Day-Salvatore, D., Abdenur, J., Bernstein, J. A., Lorey, F., Lichter-Konecki, U., Oglesbee, D., Raymond, K., Matem, D., Schimmenti, L., Rinaldo, P., Gavrilov, D. K. 2010; 157 (2): 271-275

    Abstract

    To validate a 2-tier approach for newborn screening (NBS) of remethylation defects.The original NBS dried blood spots of 5 patients with a proven diagnosis of a remethylation disorder and 1 patient with biochemical evidence of such disorder were analyzed retrospectively to determine disease ranges for methionine (Met; 4.7-8.1 micromol/L; 1 percentile of healthy population, 11.1 micromol/L), the methionine/phenylalanine ratio (Met/Phe; 0.09-0.16; 1 percentile of healthy population, 0.22), and total homocysteine (tHcy; 42-157 micromol/L; 99 percentile of normal population, 14.7 micromol/L). These preliminary disease ranges showed a sufficient degree of segregation from healthy population data, allowing the selection of cutoff values. A simple algorithm was then developed to reflex cases to a second-tier testing for tHcy, which has been applied prospectively for 14 months.A total of 86 333 NBS samples were tested between January 2007 and March 2008, and 233 of them (0.27%) met the criteria for second-tier testing of tHcy. All cases revealed concentrations of tHcy <15 micromol/L and were considered unaffected. No false-negative results have been reported with a state-wide system based on 2 combined metabolic clinics and laboratories that cover the entire Minnesota population and border areas of neighboring states.Pending more conclusive evidence from the prospective identification of additional true-positive cases, NBS for remethylation disorders appears to be feasible with existing methodologies, with only a marginal increase of the laboratory workload.

    View details for DOI 10.1016/j.jpeds.2010.02.027

    View details for Web of Science ID 000279871700023

    View details for PubMedID 20394947

  • Index of suspicion. Pediatrics in review Zadeh, N., Bernstein, J. A., Stiasny, D., Callaghan, M. U., Flores, C. E., Tytko, J. M., Mannarino, F. P., Moore, J. 2010; 31 (4): 167-172

    View details for DOI 10.1542/pir.31-4-167

    View details for PubMedID 20360413

  • Improved physician work flow after integrating sign-out notes into the electronic medical record. Joint Commission journal on quality and patient safety / Joint Commission Resources Bernstein, J. A., Imler, D. L., Sharek, P., Longhurst, C. A. 2010; 36 (2): 72-78

    Abstract

    In recent years, electronic sign-out notes have been identified as a means of enhancing the effective transfer of patient care between providers. Such a tool was developed and implemented within the electronic medical record (EMR) system, and its impact on physician work flow was assessed.A printable sign-out report was implemented within the EMR system at a tertiary academic children's hospital. Month 1 post go-live survey data were collected in June and July 2006, and 6-month post go-live survey data were collected in November and December 2006. Use of the sign-out form to document handoff data between go-live and Month 16 (September 2007) was measured using log data from the EMR. Housestaff physicians were asked to report the impact of the tool on their work flow and satisfaction with the sign-out process through a Web-based survey.The sign-out report was steadily adopted following its introduction. Between the first and second surveys, use of EMR-integrated sign-out increased from 37% to 81% of respondents for day-to-night sign-out (chi2 = 12.79, p < .001) and from 14% to 39% for night-to-day sign-out (chi 2 = 5.08, p < .05). With increased use of the report, housestaff reported less time devoted to redundant data entry and increased satisfaction with the sign-out process.EMR-integrated sign-out documents offer the advantages of other electronic network-accessible systems and can also incorporate information already in the medical record in an automated manner. Although the primary motivation for introducing standardized, EMR-integrated sign-out documents is to enhance the safety of patient handoffs, the perception of improved physician work flow is also a benefit of such an intervention.

    View details for PubMedID 20180439

  • Clinical and Molecular Heterogeneity in Patients with the CblD Inborn Error of Cobalamin Metabolism JOURNAL OF PEDIATRICS Miousse, I. R., Watkins, D., Coelho, D., Rupar, T., Crombez, E. A., Vilain, E., Bernstein, J. A., Cowan, T., Lee-Messer, C., Enns, G. M., Fowler, B., Rosenblatt, D. S. 2009; 154 (4): 551-556

    Abstract

    To describe 3 patients with the cblD disorder, a rare inborn error of cobalamin metabolism caused by mutations in the MMADHC gene that can result in isolated homocystinuria, isolated methylmalonic aciduria, or combined homocystinuria and methylmalonic aciduria.Patient clinical records were reviewed. Biochemical and somatic cell genetic studies were performed on cultured fibroblasts. Sequence analysis of the MMADHC gene was performed on patient DNA.Patient 1 presented with isolated methylmalonic aciduria, patient 3 with isolated homocystinuria, and patient 2 with combined methylmalonic aciduria and homocystinuria. Studies of cultured fibroblasts confirmed decreased synthesis of adenosylcobalamin in patient 1, decreased synthesis of methylcobalamin in patient 3, and decreased synthesis of both cobalamin derivatives in patient 2. The diagnosis of cblD was established in each patient by complementation analysis. Mutations in the MMADHC gene were identified in all patients.The results emphasize the heterogeneous clinical, cellular and molecular phenotype of the cblD disorder. The results of molecular analysis of the MMADHC gene are consistent with the hypothesis that mutations affecting the N terminus of the MMADHC protein are associated with methylmalonic aciduria, and mutations affecting the C terminus are associated with homocystinuria.

    View details for DOI 10.1016/j.jpeds.2008.10.043

    View details for Web of Science ID 000264808000020

    View details for PubMedID 19058814

  • GENOMIC ANALYSIS OF MRNA DECAY IN E. COLI WITH DNA MICROARRAYS RNA TURNOVER IN BACTERIA, ARCHAEA AND ORGANELLES Lin, P., Singh, D., Bernstein, J. A., Lin-Chao, S. 2008; 447: 47-?

    Abstract

    The decay of mRNA plays an important role in the regulation of gene expression. Although relatively ignored for many years and regarded as a simple ribonucleotide salvage pathway, mRNA decay has been established in recent years as a well-defined cellular process that plays an integral role in determining gene expression. The recent application of microarray methods to the study of diverse organisms will help us to better understand these gene regulatory circuits and the influence of transcript stability on gene expression. DNA microarray technology is the method of choice to study individual mRNA half-lives on a global scale. It is important to standardize these methods to generate reproducible and reliable results. In this chapter, we describe experimental designs for the analysis of mRNA decay on a genome-wide scale and provide detailed protocols for each experimental step. We also present an analysis of the decay of chromosomally encoded mRNAs in E. coli.

    View details for DOI 10.1016/S0076-6879(08)02203-9

    View details for Web of Science ID 000262438300003

    View details for PubMedID 19161837

  • Global analysis of Escherichia coli RNA degradosome function using DNA microarrays PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bernstein, J. A., Lin, P. H., Cohen, S. N., Lin-Chao, S. 2004; 101 (9): 2758-2763

    Abstract

    RNase E, an essential endoribonuclease of Escherichia coli, interacts through its C-terminal region with multiple other proteins to form a complex termed the RNA degradosome. To investigate the degradosome's proposed role as an RNA decay machine, we used DNA microarrays to globally assess alterations in the steady-state abundance and decay of 4,289 E. coli mRNAs at single-gene resolution in bacteria carrying mutations in the degradosome constituents RNase E, polynucleotide phosphorylase, RhlB helicase, and enolase. Our results show that the functions of all four of these proteins are necessary for normal mRNA turnover. We identified specific transcripts and functionally distinguishable transcript classes whose half-life and abundance were affected congruently by multiple degradosome proteins, affected differentially by mutations in degradosome constituents, or not detectably altered by degradosome mutations. Our results, which argue that decay of some E. coli mRNAs in vivo depends on the action of assembled degradosomes, whereas others are acted on by degradosome proteins functioning independently of the complex, imply the existence of structural features or biochemical factors that target specific classes of mRNAs for decay by degradosomes.

    View details for DOI 10.1073/pnas.0308747101

    View details for Web of Science ID 000220065300023

    View details for PubMedID 14981237

  • Life after transcription - revisiting the fate of messenger RNA TRENDS IN GENETICS Khodursky, A. B., Bernstein, J. A. 2003; 19 (3): 113-115

    Abstract

    Recently, several groups have used high-density DNA microarrays to study mRNA turnover. These new data suggest that decay contributes significantly to determining mRNA levels, and they should prompt us to refocus our attention on the regulatory potential of mRNA decay.

    View details for Web of Science ID 000181584500001

    View details for PubMedID 12615000

  • Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management. Methods in molecular biology (Clifton, N.J.) Khodursky, A. B., Bernstein, J. A., Peter, B. J., Rhodius, V., Wendisch, V. F., Zimmer, D. P. 2003; 224: 61-78

    View details for PubMedID 12710666

  • Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S., Cohen, S. N. 2002; 99 (15): 9697-9702

    Abstract

    Much of the information available about factors that affect mRNA decay in Escherichia coli, and by inference in other bacteria, has been gleaned from study of less than 25 of the approximately 4,300 predicted E. coli messages. To investigate these factors more broadly, we examined the half-lives and steady-state abundance of known and predicted E. coli mRNAs at single-gene resolution by using two-color fluorescent DNA microarrays. An rRNA-based strategy for normalization of microarray data was developed to permit quantitation of mRNA decay after transcriptional arrest by rifampicin. We found that globally, mRNA half-lives were similar in nutrient-rich media and defined media in which the generation time was approximately tripled. A wide range of stabilities was observed for individual mRNAs of E. coli, although approximately 80% of all mRNAs had half-lives between 3 and 8 min. Genes having biologically related metabolic functions were commonly observed to have similar stabilities. Whereas the half-lives of a limited number of mRNAs correlated positively with their abundance, we found that overall, increased mRNA stability is not predictive of increased abundance. Neither the density of putative sites of cleavage by RNase E, which is believed to initiate mRNA decay in E. coli, nor the free energy of folding of 5' or 3' untranslated region sequences was predictive of mRNA half-life. Our results identify previously unsuspected features of mRNA decay at a global level and also indicate that generalizations about decay derived from the study of individual gene transcripts may have limited applicability.

    View details for DOI 10.1073/pnas.112318199

    View details for Web of Science ID 000177042400020

    View details for PubMedID 12119387

  • RNase G complementation of me null mutation identifies functional interrelationships with RNase E in Escherichia coli MOLECULAR MICROBIOLOGY Lee, K., Bernstein, J. A., Cohen, S. N. 2002; 43 (6): 1445-1456

    Abstract

    The Escherichia coli endoribonucleases RNase E (Rne) and RNase G (Rng) have sequence similarity and broadly similar sequence specificity. Whereas the absence of Rne normally is lethal, we show here that E. coli bacteria that lack the rne gene can be made viable by overexpression of Rng. Rng-complemented cells accumulated precursors of 5S ribosomal RNA (rRNA) and the RNA component of RNase P (i.e. M1 RNA), indicating that normal processing of these Rne-cleaved RNAs was not restored by RNase G; additionally, neither 5S rRNA nor M1 RNA was generated from precursors by RNase G cleavage in vitro. Using DNA microarrays containing 4405 Escherichia coli open reading frames (ORFs), we identified mRNAs whose steady-state level was affected by Rne, Rng or the N-terminal catalytic domain of RNase E. Most transcript species affected by RNase E deficiency were also elevated in an rne deletion mutant complemented by Rng. However, approximately 100 mRNAs that accumulated in Rne-deficient cells were decreased by rng-complemention, thus identifying targets whose processing or degradation may be the basis for RNase E essentiality. Remarkably prominent in this group were mRNAs implicated in energy-generating pathways or in the synthesis or degradation of macromolecules.

    View details for Web of Science ID 000174710000007

    View details for PubMedID 11952897

  • Use of traditional medicine in Mongolia: a survey COMPLEMENTARY THERAPIES IN MEDICINE Bernstein, J. A., Stibich, M. A., LeBaron, S. 2002; 10 (1): 42-45

    Abstract

    To conduct a pilot investigation of the frequency with which individuals visit practitioners of Western and traditional Mongolian medicine and their motivations for making these visits.Survey based interviews were conducted in a sample of 90 adults.Darkhan, Mongolia.Measures included the annual frequency of visits to practitioners of traditional and Western medicine as well as ratings of the importance of seven factors in choosing what type of practitioner to use.During the past year, 51% of subjects interviewed had used Western services exclusively, 8% had used traditional services exclusively, and 38% had used both types of services. Users and non-users of traditional medicine did not vary in terms of age, gender, occupation or rural vs urban residence. Traditional medicine users rated the knowledge base of traditional practitioners higher than did nonusers (5.3/7 vs 4.5/7, P < 0.01). A patient's specific illness appears to be important in deciding what type of treatment he will seek.Traditional medicine appears to be a more significant component of Mongolian health care than is reported in the international literature and consequently may deserve additional attention in future studies of the country's medical system.

    View details for DOI 10.1054/ctim.2002.0508

    View details for Web of Science ID 000177550400008

    View details for PubMedID 12442822

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