Phenotypic heterogeneity of genomic disorders and rare copy-number variants.

BACKGROUND: Some copy-number variants are associated with genomic disorders with extreme phenotypic heterogeneity. The cause of this variation is unknown, which presents challenges in genetic diagnosis, counseling, and management. METHODS: We analyzed the genomes of 2312 children known to carry a copy-number variant associated with intellectual disability and congenital abnormalities, using array comparative genomic hybridization. RESULTS: Among the affected children, 10.1% carried a second large copy-number variant in addition to the primary genetic lesion. We identified seven genomic disorders, each defined by a specific copy-number variant, in which the affected children were more likely to carry multiple copy-number variants than were controls. We found that syndromic disorders could be distinguished from those with extreme phenotypic heterogeneity on the basis of the total number of copy-number variants and whether the variants are inherited or de novo. Children who carried two large copy-number variants of unknown clinical significance were eight times as likely to have developmental delay as were controls (odds ratio, 8.16; 95% confidence interval, 5.33 to 13.07; P=2.11×10(-38)). Among affected children, inherited copy-number variants tended to co-occur with a second-site large copy-number variant (Spearman correlation coefficient, 0.66; P<0.001). Boys were more likely than girls to have disorders of phenotypic heterogeneity (P<0.001), and mothers were more likely than fathers to transmit second-site copy-number variants to their offspring (P=0.02). CONCLUSIONS: Multiple, large copy-number variants, including those of unknown pathogenic significance, compound to result in a severe clinical presentation, and secondary copy-number variants are preferentially transmitted from maternal carriers. (Funded by the Simons Foundation Autism Research Initiative and the National Institutes of Health.).

Genotype-phenotype analysis of 4q deletion syndrome: proposal of a critical region.

Chromosome 4q deletion syndrome (4q- syndrome) is a rare condition, with an estimated incidence of 1 in 100,000. Although variable, the clinical spectrum commonly includes craniofacial, developmental, digital, skeletal, and cardiac involvement. Data on the genotype-phenotype correlation within the 4q arm are limited. We present detailed clinical and genetic information by array CGH on 20 patients with 4q deletions. We identified a patient who has a ∼465 kb deletion (186,770,069-187,234,800, hg18 coordinates) in 4q35.1 with all clinical features for 4q deletion syndrome except for developmental delay, suggesting that this is a critical region for this condition and a specific gene responsible for orofacial clefts and congenital heart defects resides in this region. Since the patients with terminal deletions all had cleft palate, our results provide further evidence that a gene associated with clefts is located on the terminal segment of 4q. By comparing and contrasting our patients' genetic information and clinical features, we found significant genotype-phenotype correlations at a single gene level linking specific phenotypes to individual genes. Based on these data, we constructed a hypothetical partial phenotype-genotype map for chromosome 4q which includes BMP3, SEC31A, MAPK10, SPARCL1, DMP1, IBSP, PKD2, GRID2, PITX2, NEUROG2, ANK2, FGF2, HAND2, and DUX4 genes.

Holoprosencephaly and ectrodactyly: Report of three new patients and review of the literature.

Holoprosencephaly (HPE) and ectrodactyly represent congenital malformations of the developing forebrain and developing digits, respectively. The combination of these conditions is rare, with only 15 cases known to date (12 previously reported, and 3 new cases described here). While the findings in these patients overlap with previously described genetic conditions, the similarity in phenotypes among these patients has led to the establishment of a at least one distinct syndrome: HPE, ectrodactyly, and bilateral cleft lip-palate syndrome (OMIM 300571). There has been great interest in identifying a genetic cause for the findings in patients with HPE and ectrodactyly; however the cause(s) of this rare association still remain unknown.

Purification and physico-chemical characterisation of genetically modified phytases expressed in Aspergillus awamori.

Two heterologous phytases from Aspergillus awamori and Aspergillus fumigatus obtained from submerged cultures of genetically modified fungal strains in addition to two commercially available phytase preparations (Allzyme and Natuphos phytases) were purified to homogeneity using a combination of ultrafiltration, gel filtration and ion exchange. The purified preparations were used in subsequent characterisation studies, in which Western Immunoblot analysis, pH and temperature optima, thermal stability and substrate specificity were assessed. A. fumigatus phyA phytase expressed in A. awamori exhibited activity over a broad pH range together with an increased temperature optimum, and slightly enhanced thermal stability compared to the other phytases tested, and is thus a promising candidate for animal feed applications. This particular phytase retains activity over a wide range of pH values characteristic of the digestive tract and could conceivably be more suited to the increasingly higher feed processing temperatures being utilised today, than the corresponding phytases from Aspergillus niger.

A comparison of Caribbean and non-Caribbean clients in a residential addiction treatment facility in Antigua, West Indies.

The first 50 Caribbean clients admitted to a private, multicultural, not for profit addiction treatment center in Antigua, West Indies, were compared with the first 100 non-Caribbean clients admitted. There was no significant difference in age, 38 years (18-61 years) versus 40 years (22-63 years), or gender, 74% versus 67% male. Caribbean clients were more likely to be Black, 68% versus 2%, P < .001. Caribbean clients were less likely to have a prior psychiatric diagnosis, 18% versus 43%, P < .01, or to have been in prior treatment program, 22% versus 64%, P < .001. Caribbean and non-Caribbean clients were equally likely to be polydrug users, 48% versus 50%, and to use alcohol as a primary drug, 52% versus 51%. Caribbean clients were more likely to use cocaine, 30% versus 11%, P < .01, and marijuana, 12% versus 0%, P < .001, but less likely to use heroin, 6% versus 30%, P < .001 or pills, 0% versus 8%, P < .05. Caribbean clients were less likely to have elevated MCV, 24% versus 57%, P < .001 or serum transaminases, 23% versus 46%, P < .01. Differences between groups in this multicultural setting warrant further investigation.

Buprenorphine/naloxone and methadone maintenance treatment outcomes for opioid analgesic, heroin, and combined users: findings from starting treatment with agonist replacement therapies (START).

OBJECTIVE: The objective of this secondary analysis was to explore differences in baseline clinical characteristics and opioid replacement therapy treatment outcomes by type (heroin, opioid analgesic [OA], or combined [heroin and OA]) and route (injector or non-injector) of opioid use. METHOD: A total of 1,269 participants (32.2% female) were randomized to receive one of two study medications (methadone or buprenorphine/naloxone [BUP]). Of these, 731 participants completed the 24-week active medication phase. Treatment outcomes were opioid use during the final 30 days of treatment (among treatment completers) and treatment attrition. RESULTS: Non-opioid substance dependence diagnoses and injecting differentiated heroin and combined users from OA users. Non-opioid substance dependence diagnoses and greater heroin use differentiated injectors from non-injectors. Further, injectors were more likely to be using at end of treatment compared with non-injectors. OA users were more likely to complete treatment compared with heroin users and combined users. Non-injectors were more likely than injectors to complete treatment. There were no interactions between type of opioid used or injection status and treatment assignment (methadone or BUP) on either opioid use or treatment attrition. CONCLUSIONS: Findings indicate that substance use severity differentiates heroin users from OA users and injectors from non-injectors. Irrespective of medication, heroin use and injecting are associated with treatment attrition and opioid misuse during treatment. These results have particular clinical interest, as there is no evidence of superiority of BUP over methadone for treating OA users versus heroin users.

Safe methadone induction and stabilization: report of an expert panel.

OBJECTIVES: Methadone is a well-studied, safe, and effective medication when dispensed and consumed properly. However, a number of studies have identified elevated rates of overdose and death in patients being treated with methadone for either addiction or chronic pain. Among patients being treated with methadone in federally certified opioid treatment programs, deaths most often occur during the induction and stabilization phases of treatment. To address this issue, the federal Substance Abuse and Mental Health Services Administration invited the American Society of Addiction Medicine to convene an expert panel to develop a consensus statement on methadone induction and stabilization, with recommendations to reduce the risk of patient overdose or death related to methadone maintenance treatment of addiction. METHODS: A comprehensive literature search of English-language publications (1979-2011) was conducted via MEDLINE and EMBASE. Methadone Action Group members evaluated the resulting information and collaborated in formulating the consensus statement presented here, which subsequently was reviewed by more than 100 experts in the field. RESULTS: Published data indicate that deaths during methadone induction occur because the initial dose is too high, the dose is increased too rapidly, or the prescribed methadone interacts with another drug. Therefore, the Methadone Action Group has developed recommendations to help methadone providers avoid or minimize these risks. CONCLUSIONS: Careful management of methadone induction and stabilization, coupled with patient education and increased clinical vigilance, can save lives in this vulnerable patient population.

QT interval screening in methadone maintenance treatment: report of a SAMHSA expert panel.

In an effort to enhance patient safety in opioid treatment programs, the Substance Abuse and Mental Health Saervices Administration convened a multi-disciplinary Expert Panel on the Cardiac Effects of Methadone. Panel members (Appendix A) reviewed the literature, regulatory actions, professional guidances, and opioid treatment program experiences regarding adverse cardiac events associated with methadone. The Panel concluded that, to the extent possible, every opioid treatment program should have a universal Cardiac Risk Management Plan (incorporating clinical assessment, electrocardiogram assessment, risk stratification, and prevention of drug interactions) for all patients and should strongly consider patient-specific risk minimization strategies (such as careful patient monitoring, obtaining electrocardiograms as indicated by a particular patient's risk profile, and adjusting the methadone dose as needed) for patients with identified risk factors for adverse cardiac events. The Panel also suggested specific modifications to informed consent documents, patient education, staff education, and methadone protocols.

Cloning and expression of fungal phytases in genetically modified strains of Aspergillus awamori.

In an effort to produce phytases cost-effectively, and to determine the efficiency of a novel expression system, the genes for Aspergillus awamori ( phyA) phytase and Aspergillus fumigatus ( phyA) phytase (a putative thermostable enzyme) were cloned and overexpressed in A. awamori. Regulation of phytase expression was achieved by separately placing the genes under the transcriptional control of the glucoamylase A ( glaA) promoter of A. awamori. A gene fusion strategy was employed that involved the insertion of a hexapeptide Kex-2 protease cleavage site between the native glucoamylase and heterologous proteins and allowed for the efficient secretion and processing of the resultant chimeric proteins produced in this system by an endogenous Kex-2 protease. The genes for both of the above-mentioned phytases have already been cloned; however, this is the first report of either of the two phytases being fused with the glucoamylase gene, placed under the transcriptional control of the glaA promoter and overexpressed in A. awamori. Following transformation of A. awamori with separate expression vectors (one for each phytase), induction of phytase expression in submerged culture was effected by utilisation of a starch-containing medium. Optimisation of heterologous protein production in small shake-flask cultures involved changes in medium constituents. Maximum phytase expression levels of 200 phytase units (PU) ml(-1) and 62 PU ml(-1) for recombinantly expressed phytases from A. awamori and A. fumigatus, respectively, were obtained in crude fermentation extracts. Subsequent process scale-up to 4 l batch fermentation yielded phytase production levels comparable to those obtained on small scale. The enzyme yields herein reported demonstrate that the expression system developed and the host strain utilised were capable of expressing phytase at levels comparable to, or exceeding, previously reported data.