Computational repurposing of oncology drugs through off-target drug binding interactions from pharmacological databases

PURPOSE

Systematic repurposing of approved medicines for another indication may accelerate drug development in oncology. We present a strategy combining biomarker testing with drug repurposing to identify new treatments for patients with advanced cancer.

METHODS

Tumours were sequenced with the Illumina TruSight Oncology 500 (TSO-500) platform or the FoundationOne CDx panel. Mutations were screened by two medical oncologists and pathogenic mutations were categorised referencing literature. Variants of unknown significance were classified as potentially pathogenic using plausible mechanisms and computational prediction of pathogenicity. Gain of function (GOF) mutations were evaluated through repurposing databases Probe Miner (PM), Broad Institute Drug Repurposing Hub (Broad Institute DRH) and TOPOGRAPH. GOF mutations were repurposing events if identified in PM, not indexed in TOPOGRAPH and excluding mutations with a known Food and Drug Administration (FDA)-approved biomarker. The computational repurposing approach was validated by evaluating its ability to identify FDA-approved biomarkers. The total repurposable genome was identified by evaluating all possible gene-FDA drug-approved combinations in the PM dataset.

RESULTS

The computational repurposing approach was accurate at identifying FDA therapies with known biomarkers (94%). Using next-generation sequencing molecular reports (n = 94), a meaningful percentage of patients (14%) could have an off-label therapeutic identified. The frequency of theoretical drug repurposing events in The Cancer Genome Atlas pan-cancer dataset was 73% of the samples in the cohort.

CONCLUSION

A computational drug repurposing approach may assist in identifying novel repurposing events in cancer patients with no access to standard therapies. Further validation is needed to confirm a precision oncology approach using drug repurposing.

Parental perspective of the benefits of genetic testing in children with congenital deafness

AIM

The aim of the study was to assess the perceived value of genetic testing for congenital deafness in families attending a clinical genetic outpatients department at a children's hospital. The major testing objective was to provide information regarding deafness etiology, although families were advised that changes in treatment as a result of the test were unlikely. Using a 'willingness-to-pay' approach in the form of a questionnaire developed by Ryan et al. [J Med Genet 2003;40:1-5], parents were surveyed for their attitudes and willingness to pay for genetic testing.

RESULTS

Forty-nine families provided data for analysis, representing 56% of clinic attendances throughout the period. Most of the parents were themselves unaffected by hearing loss (93%) and none were deaf, although almost a quarter (22%) reported a family member born deaf. Parents considered the major benefit gained from testing was to better achieve clarity of understanding arising from discussion and the possible ascertainment of etiology. The average sum parents were willing to pay for genetic testing was 200 Australian dollars (AUD, 2007) or approximately 123 euros (EUR), ranging from 150 to 295 AUD according to ability to pay (as measured by gross income). However, the amount that even the highest income level were willing to pay underestimated the full economic cost of genetic testing.

CONCLUSION

Genetic testing for deafness is highly valued by affected families despite the current limited overall expectation of definitive genetic diagnosis or changes in treatment. Parents considered the major benefits to be a better understanding of congenital deafness and the potential for assignment of causality.

Expanding the phenotype of Filippi syndrome: a report of three cases

This report is of two brothers and a male singleton with clinical characteristics of Filippi syndrome, born to young, healthy, non-consanguineous parents. Their features, which include borderline to milder developmental delay, particularly of speech and language, primary microdontia and previously unreported radiological findings are described to further delineate and expand the clinical spectrum of the condition.

Efficacy of gene testing for von Hippel-Lindau disease

OBJECTIVE

To determine the efficacy of genetic testing of individuals presenting with features possibly indicative of von Hippel-Lindau (VHL) disease, regardless of other relevant family and clinical details.

SETTING AND PARTICIPANTS

Between September 1994 and December 1997, 16 unrelated individuals were referred to Genetic Services of Western Australia by local clinicians and by similar genetic services in other States, for VHL gene mutation analysis because of clinical manifestations suggestive of the diagnosis.

METHODS

The subjects were investigated by screening for mutations in the polymerase chain reaction products of the three VHL gene exons using single-stranded conformational polymorphism analysis (SSCP). If no mutations were detected the exons were sequenced, and if no variations were found DNA was examined by Southern analysis for germinal rearrangements.

RESULTS

Mutations in the VHL gene were detected in eight of 16 individuals (50%), including 3 individuals with no family history suggestive of VHL disease. Five mutations were detected by SSCP, two by gene sequencing and one by Southern analysis. Each mutation occurred only in a single family and three had not been previously reported.

CONCLUSION

Genetic screening of individuals presenting with clinical features suggestive of VHL facilitates confirmation of the diagnosis, accurate genetic counselling and surveillance of at-risk family members. The necessity for costly and time-consuming screening programs can be reduced and screening directed at those carrying the mutation. Our low stringency criteria are justified for screening for VHL mutations.

Evaluation of a project to enhance knowledge of hereditary diseases and management

During 1992 and 1993, in a designated suburban area of Perth, Western Australia, information on hereditary disease was provided for health professionals and the general community. This information was in the form of posters, pamphlets, postal flyers and return letter cards, a static display, newspaper articles, advertisements and radio broadcasts, and professional seminars. The aim of this project was to evaluate the effectiveness of combined strategies to convey practical information about hereditary disease to the community and health professionals. Multiple measures of response evaluation were used, which included structured questionnaire surveys of health professionals and members of the community before and after the project. In the community surveys, respondents who were female, married, middle aged, and parents, and had a higher level of education or were born in Australia, New Zealand, or the United Kingdom were generally better informed about hereditary diseases. This intervention resulted in only meagre changes in community knowledge about hereditary disease, even though promotional materials were shown to be appropriate. General Practitioners (GPs) and Child Health Nurses (CHNs) were supportive of clinical genetic services and recognised a need for continuation of education in this field. There is a rapidly increasing need for community and health professional comprehension of the applications of the new genetic technology. This project indicates that routine educational and health promotion strategies will not be enough to achieve desired levels of knowledge and attitude change.

The clinical correlates of a 3' truncating mutation (codons 1982-1983) in the adenomatous polyposis coli gene

Familial adenomatous polyposis (FAP) is caused by mutations in the adenomatous polyposis coli (APC) gene, and different mutations may produce different clinical pictures. Most mutations occur in the 5' half of the gene, and mutations toward the 3' end are rare. The aim of this study was to document the phenotypes in a family with a truncating mutation at codons 1982-1983, one of the most 3' mutations on record. Colonic polyps in this family were much less numerous, and their growth was delayed compared with the classical FAP picture, and malignant degeneration occurred considerably later. Two individuals had sparse colonic but profuse gastric fundic gland polyposis. Gardner's syndrome stigmata were variable, and a desmoid tumor was recorded in 1 person.

Genetic counselling and gene mutation analysis in familial adenomatous polyposis in Western Australia

OBJECTIVE

To assess the provision of accurate pre-symptomatic genetic testing with DNA analysis and appropriate counselling for individuals and families known to be at high risk of developing familial adenomatous polyposis coli (FAP).

PATIENTS AND METHODS

Thirty-one families with clinically and pathologically documented FAP were ascertained from the Western Australian Polyposis Registry. DNA was collected from over 200 individuals in these families to establish their genetic risk status for FAP, either by direct mutation analysis, or by linkage analysis. Individuals undergoing DNA testing were given intensive psychosocial support and counselling.

RESULTS

In 19 families DNA-based counselling could not be offered because either the adenomatous polyposis coli (APC) gene mutation could not be detected or there were insufficient family members for linkage analysis. Gene testing yielded mutations of the APC gene in 87 individuals from 12 families; by gene tracking (or linkage analysis) in three families and by mutation analysis in the remaining nine (four of which had only one affected individual). DNA results conformed with a definite clinicopathological diagnosis in 27 FAP patients and, of the remaining 60 high-risk subjects tested, 14 had inherited the mutated APC gene.

CONCLUSIONS

DNA analysis allowed accurate genetic counselling for 12 of 31 families affected by FAP, thus improving the medical and personal management in asymptomatic people who would otherwise be subjected to the uncertainty of long term surveillance and repeated colonic examinations. In future a superior biomolecular approach to gene mutation analysis, such as the protein truncation test, will facilitate management for most FAP individuals and families.

Mutation analysis of Western Australian families affected by cystic fibrosis

OBJECTIVE

To document the results of mutation analysis on 160 individuals with cystic fibrosis and 31 obligate carriers of the cystic fibrosis gene in 191 Western Australian families to facilitate accurate genetic counselling.

METHODS

We tested for 17 mutations of the cystic fibrosis gene by either a variation of the polymerase chain reaction amplification refractory mutation system (PCR-ARMS) or with a series of restriction enzyme cuts and dot blots using chemiluminescent probes.

RESULTS

At least one of the two intragenic mutations causing cystic fibrosis was identified in 98% of affected individuals and both were detected in 68%. The delta F508 deletion occurred in 89.8% of patients: 51% were homozygous for this defect. In carriers, 85% of the mutations were detected with a panel of 16 probes, identifying 17 intragenic defects: the delta F508 deletion occurred in 72.4%. Both cystic fibrosis mutations were detected in 68% of cystic fibrosis families.

CONCLUSIONS

By analysis with 16 intragenic cystic fibrosis genomic probes, we have documented the frequencies of various mutations in the Western Australian population. These data will be useful in accurate genetic counselling for affected families and carrier screening for the general population.

Improving diagnosis of Huntington's disease by analysis of an intragenic trinucleotide repeat expansion

OBJECTIVE

To develop an accurate presymptomatic test for Huntington's disease.

METHOD

An improved polymerase chain reaction method was used to investigate the pattern of expansions of a CAG repeat sequence located in the 5' region of a gene recently found to produce the protein called Huntingtin. We documented the range of trinucleotide repeat expansions in the responsible gene in 82 affected individuals compared with 80 control subjects from a Western Australian population.

RESULTS

The number of expanded repeats ranged from 40 to 73 in affected individuals and from 13 to 38 in normal controls.

CONCLUSIONS

Polymerase chain reaction analysis of a CAG repeat sequence in the Huntington's disease gene clearly differentiated between normal and mutated alleles, providing an accurate diagnostic test for the disorder in individuals at risk. This predictive test has met with greater acceptance and demand than methods using family based linkage studies.

The limitation of referral level fetal ultrasound examination in the detection of spina bifida in Western Australia, 1990-1991

OBJECTIVE

To ascertain babies born with spina bifida that was not detected by prenatal ultrasound examination performed after 16 weeks' gestational age at Western Australian referral centres, 1990-1991.

DESIGN

A retrospective study of the antenatal ultrasound details of those infants born with spina bifida in Western Australia during the 24-month period, 1990 and 1991. Data were collected by interviewing parents, clinically assessing affected individuals and reviewing genetic, clinical and investigative records, and from the Birth Defects Registry of Western Australia.

SETTING

Western Australia, which has a relatively high spina bifida birth prevalence of 1 in 1000, has centralised neonatal medical, surgical and genetic services, and a Birth Defects Registry. This enabled us to ascertain all Western Australian neonates with spina bifida for the purposes of this study. There is no universal maternal serum alpha-fetoprotein (MSAFP) screening program and the performance of ultrasonography at referral level is of variable quality.

PARTICIPANTS

Newborns with spina bifida and their parents.

MAIN OUTCOME MEASURES

Ultrasound screening for spina bifida was deemed to have failed when referral to a specialist imaging centre for the specific purpose of detecting anatomical abnormality after 16 weeks' gestational age gave a falsely negative result.

RESULTS

Of the 47 infants born with spina bifida in 1990 and 1991, ultrasound screening at more than 16 weeks' gestational age was documented and was falsely negative in 14. Six of the 14 had a relevant family or medical history for the condition. Five of the lesions were covered and eight of the patients still survive.

CONCLUSION

Ad-hoc fetal ultrasound examination via existing referral centres had obvious limitations in detecting spina bifida in a population at low risk. MSAFP screening has a well documented role in detecting neural tube defects, as eight to 10 of the 14 lesions missed by the referral ultrasonography would have been ascertained in a program of this nature. The study indicated that adequate pre-screening clinical histories were not sought, thus limiting the antenatal testing options offered to at-risk couples. This study emphasised the importance of a statewide review of the specificity and sensitivity of the anatomical fetal ultrasound examination, in view of the expansion of this procedure and its variable quality depending on operator experience and equipment quality.

Tyrosinase positive albinism with familial 46,XY,t(2;4) (q31.2;q31.22) balanced translocation

A subject with clinical and biochemical tyrosinase positive oculocutaneous albinism (OCA) also had a balanced translocation, 46,XY,t(2;4)(q31.2;q31.22). This observation provides evidence for a possible gene locus in the q31 region of chromosome 2 or 4.

Congenital toxoplasmosis: a large survey in western Australia

OBJECTIVE

To determine the birth prevalence of congenital toxoplasmosis in Western Australia.

DESIGN

A prospective serological study of randomly selected pregnant women and their newborn infants. Paired sera collected from the mothers at their first antenatal visit and cord blood specimens taken from their infants were tested for toxoplasmosis by the direct agglutination test and Toxoplasma IgM-capture enzyme-linked immunosorbent assay.

SETTING

A major Perth metropolitan obstetric teaching hospital where approximately one-quarter of infants born in Western Australia during January 1986 to December 1989 inclusive were delivered.

PARTICIPANTS

Sera were obtained from 10,207 pregnant women presenting for routine clinical evaluation at their first antenatal visit. Cord blood specimens were taken from 18,908 infants; 7523 of these could be paired to maternal specimens.

MAIN OUTCOME MEASURES

Maternal infection was indicated in cases where Toxoplasma specific IgM antibody was present or where an initial maternal specimen gave negative results for Toxoplasma antibody but the paired cord blood specimen gave positive results. Toxoplasma specific IgM antibody in a cord blood specimen indicated fetal infection.

RESULTS

Of the 10,207 women 3544 (35%) were Toxoplasma immune at their first antenatal visit; in 11 Toxoplasma specific IgM antibody was detected. There was no serological or clinical evidence of congenital toxoplasmosis in any of the offspring of these 11 mothers. The rate of maternal infection in susceptible pregnancies was 1.6 per 1000; the maternal-fetal transmission rate was estimated to be no greater than 24%. Three of the 18,908 cord blood specimens tested gave positive results for Toxoplasma specific IgM antibody giving a birth prevalence of congenital infection of 0.23 per 1000 births to non-immune mothers. There were no clinical features of congenital infection in these three infants but they will require long-term follow-up. Thirteen of the 14 mothers infected during pregnancy were interviewed retrospectively and in only three was a known risk factor for infection present.

CONCLUSIONS

a toxoplasmosis screening programme for pregnant mothers is not justifiable in Western Australia. A public education programme is also likely to have limitations.

Dandy-Walker malformation (variant), cystic dysplastic kidneys, and hepatic fibrosis: a distinct entity or Meckel syndrome?

Dandy-Walker malformation is an unusual finding in Meckel syndrome, which characteristically presents with encephalocele, polydactyly, and cystic renal disease. We report on a family in which three nonviable brothers had Dandy-Walker malformations (variant) with associated enlarged cystic dysplastic kidneys and hepatic fibrosis. The consistent segregation of these abnormalities in all three sibs in the absence of polydactyly and encephalocele suggested the possibility of a distinct syndrome. The clinicopathological findings of the disorder are described and discussed in the context of the phenotypic spectrum of Meckel syndrome.

Rapp-Hodgkin hypohidrotic ectodermal dysplasia syndrome

Four members in three generations of a family had Rapp-Hodgkin hypohidrotic ectodermal dysplasia syndrome with variable involvement of teeth, hair, nails and palate, characteristic facies and mild heat tolerance problems. In addition, the proband had a high sweat sodium, hypogenitalism, hypothelia and marked cicatricial scalp atrophy and scarring. Inheritance of the condition was consistent with an autosomal dominant mode and the manifestations are described to delineate further this rare phenotype.

The Nance-Horan syndrome

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Autosomal dominant osteopetrosis type II with "malignant" presentation: further support for heterogeneity?

The osteopetroses are a heterogeneous group of disorders characterised by generalised bony sclerosis. The autosomal dominant form usually has a "benign" prognosis, in contrast to the "malignant" course of the autosomal recessive variety. In this paper we describe a kindred in which the phenotypic spectrum varied from an asymptomatic condition in adults to a severely affected infant, presenting with anaemia, hepatosplenomegaly, hydrocephalus and blindness. The findings in this family are reported and discussed to elucidate further the possible genetic heterogeneity in autosomal dominant osteopetrosis.

Clinical considerations in Buschke-Ollendorff syndrome

This brief report describes a mother and two daughters with the rare Buschke-Ollendorff syndrome. That the typical dermal connective tissue naevi lesions may become less obvious with time and that the condition is not always so "benign" are important clinical features not well recognised. Incorrect diagnosis may lead to embarkation upon hazardous management.

Juvenile polyposis: a case with early presentation and death attributable to adenocarcinoma of the pancreas

A male child who first presented in the second year of life demonstrated all the recognized clinicopathological manifestations of juvenile polyposis with associated birth defects. Subsequent death at age 19 years from adenocarcinoma of the pancreas further broadens the recognized spectrum of possible sequelae in this disorder and is in keeping with current hypotheses of inherent cancer potential throughout the polyposis syndromes.

Acute chromium poisoning in a 2 year old child

Sodium dichromate ingestion in children is uncommon and potentially lethal. The most appropriate management is uncertain because of the lack of sound data contained in the few reports of successfully treated patients. Immediate treatment should include urgent induction of emesis, administration of ascorbic acid as an antidote, followed by supportive treatment.

Some epidemiological aspects of pyloric stenosis in British Columbia

The records of an ongoing Health Surveillance Registry that utilizing multiple sources of ascertainment were used to study the incidence rate of infantile hypertrophic pyloric stenosis (IHPS) in liveborn children in British Columbia during the period 1966--1977 inclusive. The incidence was 4.6 male/1,000 livebirths and 1.2 females/1,000 livebirths, giving a male to female ratio of 3.1 to 1. No significant overall incidence variations with time could be shown during the study period. There was suggestive evidence of independent sex-incidence variation in different geographical regions, which clearly warrants further investigation.

Lack of breast feeding and early weaning in infants of Asian immigrants to Wolverhampton

Fifty Asian immigrant mothers who would have expected to breast feed their infants had they remained in rural Asia were studied. There was a striking reduction in the incidence and duration of breast feeding on arrival in the United Kingdom, and a fall in the age of weaning. The availability of an alternative to human milk is the most important factor reducing the incidence of breast feeding. Only 2 (4%) of the 46 infants followed prospectively were breast fed. Reasons for not breast feeding were sought and the results indicated that the majority of mothers were frightened, misinformed, or apathetic about breast feeding. If breast feeding is to be promoted, antenatal education and encouragement is essential. The advantages of human milk need to be stressed. Potentially serious mistakes occurred in preparing bottle feeds, and vitamin supplements were often inadequate. Later weaning could be encouraged by the staff of well baby clinics.