Lyn Schofield

Population-based detection of lynch syndrome in young colorectal cancer patients using microsatellite instability as the initial test

Approximately 1–2% of colorectal cancers (CRC) arise because of germline mutations in DNA mismatch repair genes, referred to as Lynch syndrome. These tumours show microsatellite instability (MSI) and loss of expression of mismatch repair proteins. Pre‐symptomatic identification of mutation carriers has been demonstrated to improve survival; however, there is concern that many are not being identified using current practices. We evaluated population‐based MSI screening of CRC in young patients as a means of ascertaining mutation carriers. CRC diagnosed in patients aged <60 years were identified from pathology records. No prior information was available on family history of cancer. PCR techniques were used to determine MSI in the BAT‐26 mononucleotide repeat and mutation in the BRAF oncogene. Loss of MLH1, MSH2, MSH6 and PMS2 protein expression was evaluated in MSI+ tumours by immunohistochemistry. MSI+ tumours were found in 105/1,344 (7.8%) patients, of which 7 were excluded as possible Lynch syndrome because of BRAF mutation. Of the 98 “red flag” cases that were followed up, 25 were already known as mutation carriers or members of mutation carrier families. Germline test results were obtained for 35 patients and revealed that 22 showed no apparent mutation, 11 showed likely pathogenic mutations and 2 had unclassified variants. The proportion of MSI+ cases in different age groups that were estimated to be mutation carriers was 89% (<30 years), 83% (30–39), 68% (40–49) and 17% (50–59). We recommend MSI as the initial test for population‐based screening of Lynch syndrome in younger CRC patients, regardless of family history.

A Germline MTOR Mutation in Aboriginal Australian Siblings with Intellectual Disability, Dysmorphism, Macrocephaly, and Small Thoraces

We report on three Aboriginal Australian siblings with a unique phenotype which overlaps with known megalencephaly syndromes and RASopathies, including Costello syndrome. A gain‐of‐function mutation in MTOR was identified and represents the first reported human condition due to a germline, familial MTOR mutation. We describe the findings in this family to highlight that (i) the path to determination of pathogenicity was confounded by the lack of genomic reference data for Australian Aboriginals and that (ii) the disease biology, functional analyses in this family, and studies on the tuberous sclerosis complex support consideration of an mTOR inhibitor as a therapeutic agent.

Population-based screening for Lynch syndrome in Western Australia

We showed earlier that routine screening for microsatellite instability (MSI) and loss of mismatch repair (MMR) protein expression in colorectal cancer (CRC) led to the identification of previously unrecognized cases of Lynch syndrome (LS). We report here the results of screening for LS in Western Australia (WA) during 1994–2012. Immunohistochemistry (IHC) for loss of MMR protein expression was performed in routine pathology laboratories, while MSI was detected in a reference molecular pathology laboratory. Information on germline mutations in MMR genes was obtained from the states single familial cancer registry. Prior to the introduction of routine laboratory‐based screening, an average of 2–3 cases of LS were diagnosed each year amongst WA CRC patients. Following the implementation of IHC and/or MSI screening for all younger (<60 years) CRC patients, this has increased to an average of 8 LS cases diagnosed annually. Based on our experience in WA, we propose three key elements for successful population‐based screening of LS. First, for all younger CRC patients, reflex IHC testing should be carried out in accredited pathology services with ongoing quality control. Second, a state‐ or region‐wide reference laboratory for MSI testing should be established to confirm abnormal or suspicious IHC test results and to exclude sporadic cases by carrying out BRAF mutation or MLH1 methylation testing. Finally, a state or regional LS coordinator is essential to ensure that all appropriate cases identified by laboratory testing are referred to and attend a Familial Cancer Clinic for follow‐up and germline testing.

Impact of Clinical Genetics Attendance at a Gynecologic Oncology Tumor Board on Referrals for Genetic Counseling and BRCA Mutation Testing.

Objectives The objectives of this work were to determine the proportion of eligible patients with ovarian cancer discussed at a gynecologic oncology tumor board who were referred for counseling and BRCA mutation testing; to compare referral rates before genetics attendance at the tumor board to referral rates after genetics attendance; and to ascertain the proportions of women with germline BRCA mutations. Materials and Methods Eligible cases were identified from the minutes of the weekly Western Australian gynecologic oncology tumor board from July 1, 2013 to June 30, 2015. Patients with ovarian cancer who met eligibility criteria for genetics referral were identified and checked against the records of the genetic services database to ascertain whether a referral was received. Outcomes including attendance for counseling and results of mutation testing were analyzed. Results Two hundred sixty-one patients were eligible for referral during the 24-month study period. One hundred six patients (40.6%) were referred for counseling and germline mutation testing. Of the eligible patients, 26.7% were referred in the 12 months before genetics attendance at the tumor board compared to 51.7% of the eligible patients in the 12 months after genetics attendance (P ≤ 0.0001). Ninety-seven patients were offered BRCA mutation testing, and 73 underwent testing with 65 results reported to date. Twenty-two patients (33.8 %) tested positive for a germline BRCA mutation. Conclusions Patients with ovarian cancer had a high rate of BRCA mutations. Attendance of a genetics service at a tumor board was associated with an improved rate of referral of patients for genetic counseling and BRCA mutation testing.

Craniometaphyseal dysplasia and chondrocalcinosis cosegregating in a family with an ANKH mutation

Mutations in ANKH have been associated with craniometaphyseal dysplasia (CMD) in some families [N€ urnberg et al., 2001; Reichenberger et al., 2001] and with familial chondrocalcinosis (CCAL2) in others [Pendleton et al., 2002; Williams et al., 2003]. We report on the first family with an ANKH mutation in which these conditions cosegregated in some affected family members to promote awareness of the possibility that individuals with CMD might have associated chondrocalcinosis. A 22-month-old boy from a family, previously reported by Taylor and Sprague [1989] and as part of ‘‘family 7’’ by N€ urnberg et al. [2001], with a known ANKH mutation (G389R) was referred for genetic consultation when he presented with choanal stenosis and radiographic evidence of CMD. His 30-year-old father had the familial mutation and manifested a slowly progressive unilateral facial nerve palsy (Fig. 1) and had no discrete episodes of pain. His two mutation-positive brothers were asymptomatic. The paternal grandmother (III-9), age 57, also had the familial mutation and she had bilateral facial nerve palsy (Fig. 2), mild hearing loss and a history of episodic unilateral shoulder pain from her 20s, with radiographically confirmed ectopic calcification, treated by surgical excision at age 22; the original radiograph was not accessible for review. She had additional episodic pain of the small joints of her hands, particularly at the second and third metacarpals (Fig. 3); in her feet, particularly at the left second and third metatarsals; and knees. A technetium bone scan demonstrated intense uptake of tracer involving the left 2nd and 3rd tarsometatarsal and the left 2nd metatarsophalangeal (MTP) joints confirming a marked focal arthropathy with mild synovitis of these joints; there was mild uptake of both first MTPs consistent with a mild arthropathy. She also had excision of an exostosis of the left knee in her 30s. A mutation positive sister and a mutation positive half-sister had similar symptoms. Subject III-1, age 68 years, described episodic, excruciating joint pains typically lasting 48 hr, with onset in her late 20s, affecting predominantly her left shoulder, elbow, and left ankle. Subject (III-7), age 53, described episodic, excruciating pain of a similar duration, from the age of 26 years, affecting the metacarpophalangeal joint of her left thumb, the distal interphalangeal (DIP) joints of her right hand and the DIP joint of her left second toe, both shoulders, and elbows. She described that the affected joints of her hands were red and swollen at the times of pain and that there was occasional spontaneous clear, sticky discharge from the DIP joint of her right third finger. Calcium deposits were excised from her shoulder and elbow joints in her 30s and calcium hydroxyapatite crystals were present in the synovial fluid. Due to considerable time between diagnosis, treatment, and genetic consultation, no radiographs were available for review. A mutation positive half-sister, who was unavailable for clinical assessment, was described as having pain of a similar nature. No other relatives in this generation were available for review. The paternal great grandmother was described as having adult onset hearing loss and episodic joint pain, which at times was debilitating, and predominantly affected hands and feet. There was no known history consistent with chondrocalcinosis in other relatives. ANKH (a homologue of murine Ank) encodes a transmembrane protein that transports pyrophosphate (PPi) across the plasma membrane [Gurley et al., 2006]. Spontaneous mutations in Ank were associated with deposition of hydroxyapatite in articular cartilage and synovial fluid, and ankylosis [Hakim et al., 1984; Sampson, 1988]. Subsequently, mutations in ANKH were identified independently in individuals with CMD and

Initiating an undiagnosed diseases program in the Western Australian public health system

BackgroundNew approaches are required to address the needs of complex undiagnosed diseases patients. These approaches include clinical genomic diagnostic pipelines, utilizing intra- and multi-disciplinary platforms, as well as specialty-specific genomic clinics. Both are advancing diagnostic rates. However, complementary cross-disciplinary approaches are also critical to address those patients with multisystem disorders who traverse the bounds of multiple specialties and remain undiagnosed despite existing intra-specialty and genomic-focused approaches. The diagnostic possibilities of undiagnosed diseases include genetic and non-genetic conditions. The focus on genetic diseases addresses some of these disorders, however a cross-disciplinary approach is needed that also simultaneously addresses other disorder types. Herein, we describe the initiation and summary outcomes of a public health system approach for complex undiagnosed patients - the Undiagnosed Diseases Program-Western Australia (UDP-WA).ResultsBriefly the UDP-WA is: i) one of a complementary suite of approaches that is being delivered within health service, and with community engagement, to address the needs of those with severe undiagnosed diseases; ii) delivered within a public health system to support equitable access to health care, including for those from remote and regional areas; iii) providing diagnoses and improved patient care; iv) delivering a platform for in-service and real time genomic and phenomic education for clinicians that traverses a diverse range of specialties; v) retaining and recapturing clinical expertise; vi) supporting the education of junior and more senior medical staff; vii) designed to integrate with clinical translational research; and viii) is supporting greater connectedness for patients, families and medical staff.ConclusionThe UDP-WA has been initiated in the public health system to complement existing clinical genomic approaches; it has been targeted to those with a specific diagnostic need, and initiated by redirecting existing clinical and financial resources. The UDP-WA supports the provision of equitable and sustainable diagnostics and simultaneously supports capacity building in clinical care and translational research, for those with undiagnosed, typically rare, conditions.

3-Dimensional Facial Analysis—Facing Precision Public Health

Precision public health is a new field driven by technological advances that enable more precise descriptions and analyses of individuals and population groups, with a view to improving the overall health of populations. This promises to lead to more precise clinical and public health practices, across the continuum of prevention, screening, diagnosis, and treatment. A phenotype is the set of observable characteristics of an individual resulting from the interaction of a genotype with the environment. Precision (deep) phenotyping applies innovative technologies to exhaustively and more precisely examine the discrete components of a phenotype and goes beyond the information usually included in medical charts. This form of phenotyping is a critical component of more precise diagnostic capability and 3-dimensional facial analysis (3DFA) is a key technological enabler in this domain. In this paper, we examine the potential of 3DFA as a public health tool, by viewing it against the 10 essential public health services of the “public health wheel,” developed by the US Centers for Disease Control. This provides an illustrative framework to gage current and emergent applications of genomic technologies for implementing precision public health.

A child with an STK11 mutation and Sotos syndrome-like features: can STK11 mutations produce a Sotos syndrome phenocopy?

In accordance with interrelationships between tumour predisposition and somatic overgrowth, the authors present a boy with a familial serine threonine kinase 11 (STK11) mutation and Sotos syndrome-like features. The authors suggest that, analogous to phosphatase and tensin homolog mutations, STK11 mutations may predispose to somatic overgrowth. In a minority of instances, this may result in a Sotos syndrome phenocopy. If substantiated, this observation may yield insights into both the molecular causes of tumour predisposition and overgrowth syndromes.

Investigating barriers to genetic counseling and germline mutation testing in women with suspected hereditary breast and ovarian cancer syndrome and Lynch syndrome

OBJECTIVE The aim of the current study was to explore barriers to genetic counseling and testing in women with gynecological cancers deemed at significant risk of carrying a germline mutation. METHODS A qualitative study using semi-structured interviews and inductively analysed thematically. Eight patients with ovarian or endometrial cancer participated in individual semi-structured telephone interviews that assessed motivation for genetic counseling and testing, perceived benefits and barriers, timing of the approach, perceptions of the referral process to genetic services and locus of control in relation to cancer and health. RESULTS Analysis of the interview transcripts revealed five themes relating to perceptions of genetic counseling and testing: Lack of importance; Level of information received; Timing of referral processes; Fear and anxiety; Resistance to and perceptions of counseling. CONCLUSIONS Participants had a limited understanding of hereditary cancer syndromes and did not appreciate the benefits of genetic testing. A consistent approach at the time of referral to genetic services is needed to ensure that the level and format of information is appropriate for patients. PRACTICE IMPLICATIONS The rationale for genetic testing needs to be better explained to patients and the timing of referral should be based both on treatment priorities and patient preferences.

State-wide population screening for Lynch syndrome? Improved ascertainment of at risk families

We have previously established in a large retrospective study that MSI testing was an effective first screen for the identification of individuals with Lynch syndrome (LS) in colorectal cancer (CRC) patients aged < 60 years. From these findings, MSI and/or IHC screening was recommended for all newly diagnosed CRC patients aged < 60 years in Western Australia, regardless of family history of cancer. We have subsequently evaluated the utility of routine MSI/IHC screening in diagnostic pathology laboratories for the detection of previously undiagnosed individuals and families with LS. From January 2009 to December 2010, 270 tumours were tested for MSI and expression of MLH1, PMS2, MSH2 and MSH6 using IHC. Cases showing MSI and/ or loss of expression were also tested for BRAF V600E mutation. Seventy cases were found to have MSI, of which 25 were excluded from further investigation as possible LS cases due to the presence of the BRAF V600E mutation. The remaining 45 “red flag” cases were eligible for germline testing based on their MSI, IHC and BRAF status. From 26 cases tested to date, 11 germline mutations have been found. Nine were from individuals not previously recognized as LS and two were untested members from known LS families. Extrapolation of the mutation incidence (11/26, 42%) to all red flag cases (n=45) suggests approximately 19 mutation carriers in this cohort. This value approximates the number of LS cases that could be expected to arise in the Western Australian population over a two-year period (n=24), assuming that 1% of all CRCs are due to LS. Our preliminary findings following the implementation of state-wide routine MSI and IHC testing in Western Australia indicate that the majority of LS cases are being identified.