Combinatorial batching of DNA for ultralow-cost detection of pathogenic variants.

BACKGROUND: Next-generation sequencing (NGS) based population screening holds great promise for disease prevention and earlier diagnosis, but the costs associated with screening millions of humans remain prohibitive. New methods for population genetic testing that lower the costs of NGS without compromising diagnostic power are needed. METHODS: We developed double batched sequencing where DNA samples are batch-sequenced twice - directly pinpointing individuals with rare variants. We sequenced batches of at-birth blood spot DNA using a commercial 113-gene panel in an explorative (n = 100) and a validation (n = 100) cohort of children who went on to develop pediatric cancers. All results were benchmarked against individual whole genome sequencing data. RESULTS: We demonstrated fully replicable detection of cancer-causing germline variants, with positive and negative predictive values of 100% (95% CI, 0.91-1.00 and 95% CI, 0.98-1.00, respectively). Pathogenic and clinically actionable variants were detected in RB1, TP53, BRCA2, APC, and 19 other genes. Analyses of larger batches indicated that our approach is highly scalable, yielding more than 95% cost reduction or less than 3 cents per gene screened for rare disease-causing mutations. We also show that double batched sequencing could cost-effectively prevent childhood cancer deaths through broad genomic testing. CONCLUSIONS: Our ultracheap genetic diagnostic method, which uses existing sequencing hardware and standard newborn blood spots, should readily open up opportunities for population-wide risk stratification using genetic screening across many fields of clinical genetics and genomics.

Model for ASsessing the value of Artificial Intelligence in medical imaging (MAS-AI).

OBJECTIVES: Artificial intelligence (AI) is seen as a major disrupting force in the future healthcare system. However, the assessment of the value of AI technologies is still unclear. Therefore, a multidisciplinary group of experts and patients developed a Model for ASsessing the value of AI (MAS-AI) in medical imaging. Medical imaging is chosen due to the maturity of AI in this area, ensuring a robust evidence-based model. METHODS: MAS-AI was developed in three phases. First, a literature review of existing guides, evaluations, and assessments of the value of AI in the field of medical imaging. Next, we interviewed leading researchers in AI in Denmark. The third phase consisted of two workshops where decision makers, patient organizations, and researchers discussed crucial topics for evaluating AI. The multidisciplinary team revised the model between workshops according to comments. RESULTS: The MAS-AI guideline consists of two steps covering nine domains and five process factors supporting the assessment. Step 1 contains a description of patients, how the AI model was developed, and initial ethical and legal considerations. In step 2, a multidisciplinary assessment of outcomes of the AI application is done for the five remaining domains: safety, clinical aspects, economics, organizational aspects, and patient aspects. CONCLUSIONS: We have developed an health technology assessment-based framework to support the introduction of AI technologies into healthcare in medical imaging. It is essential to ensure informed and valid decisions regarding the adoption of AI with a structured process and tool. MAS-AI can help support decision making and provide greater transparency for all parties.

Cohort profile and heritability assessment of familial pancreatic cancer: a nation-wide study.

BACKGROUND: Familial Pancreatic Cancer (FPC) is responsible for up to 10% of all cases of pancreatic ductal adenocarcinoma (PDAC). Individuals predisposed for FPC have an estimated lifetime risk of 16-39% of developing PDAC. While heritability of PDAC has been estimated to be 36% in a Nordic twin study, no heritability estimate specific on FPC has been reported. METHODS: A national cohort of Danish families with predisposition for FPC is currently included in a screening program for PDAC at Odense University Hospital. Family members included in the screening program were interviewed for pedigree data including: cases of PDAC among first-degree relatives (FDRs) and number of affected/unaffected siblings. Heritability for FPC in the predisposed families was assessed by doubling the estimated intra-class correlation coefficient (ICC) from a random intercept logistic model fitted to data on FDRs. RESULTS: Among families with predisposition for FPC, 83 cases of PDAC were identified. The median age at diagnosis of PDAC was 66 years, and median time from diagnosis to death was 7.6 months. A total of 359 individuals were found as unaffected FDRs of the 83 PDAC cases. The retrieved FDRs included a total of 247 individuals in sibship and 317 individuals in parent-offspring relatedness. We estimated an ICC of 0.25, corresponding to a narrow sense additive heritability estimate of 0.51 in the FPC family cohort. CONCLUSION: We have established a nation-wide cohort of FPC families to facilitate clinical and genetic studies on FPC. The estimated heritability of 51% prominently underlines a strong genetic background of FPC.

Is screening for pancreatic cancer in high-risk groups cost-effective? - Experience from a Danish national screening program.

OBJECTIVE: Pancreatic cancer (PC) is the fourth leading cause of cancer death worldwide, symptoms are few and diffuse, and when the diagnosis has been made only 10-15% would benefit from resection. Surgery is the only potentially curable treatment for pancreatic cancer, and the prognosis seems to improve with early detection. A hereditary component has been identified in 1-10% of the PC cases. To comply with this, screening for PC in high-risk groups with a genetic disposition for PC has been recommended in research settings. DESIGN: Between January 2006 and February 2014 31 patients with Hereditary pancreatitis or with a disposition of HP and 40 first-degree relatives of patients with Familial Pancreatic Cancer (FPC) were screened for development of Pancreatic Ductal Adenocarcinoma (PDAC) with yearly endoscopic ultrasound. The cost-effectiveness of screening in comparison with no-screening was assessed by the incremental cost-utility ratio (ICER). RESULTS: By screening the FPC group we identified 2 patients with PDAC who were treated by total pancreatectomy. One patient is still alive, while the other died after 7 months due to cardiac surgery complications. Stratified analysis of patients with HP and FPC provided ICERs of 47,156 US$ vs. 35,493 US$ per life-year and 58,647 US$ vs. 47,867 US$ per QALY. Including only PDAC related death changed the ICER to 31,722 US$ per life-year and 42,128 US$ per QALY. The ICER for patients with FPC was estimated at 28,834 US$ per life-year and 38,785 US$ per QALY. CONCLUSIONS: With a threshold value of 50,000 US$ per QALY this screening program appears to constitute a cost-effective intervention although screening of HP patients appears to be less cost-effective than FPC patients.

Cost-effectiveness of surveillance programs for families at high and moderate risk of hereditary non-polyposis colorectal cancer.

OBJECTIVES: Surveillance programs are recommended to both families at high risk (Amsterdam-positive families with known- and unknown mutation) and moderate risk (families not fulfilling all Amsterdam criteria) of colorectal cancer (CRC). Cost-effectiveness has so far only been estimated for the group at high risk. The aim of the present study is to determine cost-effectiveness of surveillance programs where families at both high and moderate risk of HNPCC participate. METHODS: A decision analytic model (Markov model) is developed to assess surveillance programs where families at high and moderate risk of HNPCC are offered surveillance from age 25 and age 45, respectively. The model includes costs for all families referred to genetic counseling, including genetic risk assessment, mutation analysis, and surveillance in relevant families with or without known mutation, plus the costs related to any surgical treatment. The risk of metachronous CRC is also modeled. RESULTS: Incremental costs per life year gained are estimated to be euro 980 when families at both high and moderate risk of HNPCC undergo surveillance (euro 508 for high risk and euro 1600 for moderate risk) and euro 1947 when the moderate risk group is evaluated genetically but not offered surveillance. Sensitivity analysis showed these findings to be robust, although cost-effectiveness can be improved in cases of more conservative referrals to genetic counseling. CONCLUSIONS: The result for high risk families confirms the findings in similar studies. Somewhat surprisingly, cost-effectiveness improves when surveillance of the moderate risk groups are included in the decision model.

The importance of functional testing in the genetic assessment of Muir-Torre syndrome, a clinical subphenotype of HNPCC.

A majority of families with hereditary nonpolyposis colorectal cancer (HNPCC) are attributable to germline mutations in three DNA mismatch repair (MMR) genes, MLH1, MSH2 and MSH6. However, the clinical phenotype appears to reflect a complex interplay between the predisposing mutation and putative constitutional and somatic modifiers. Certain MMR gene mutations predispose to combined occurrence of cutaneous sebaceous gland neoplasms and visceral malignancies, which is known as Muir-Torre syndrome (MTS) and regarded as a phenotypic variant of HNPCC. The sebaceous tumors associated with MTS appear in many patients before visceral malignancies providing important predictability of HNPCC-related integral cancers in mutation carriers. Since most sebaceous skin tumors are, however, sporadic, the contribution of non-truncating mutations found in skin cancer patients is difficult to interpret and genetic assessment of MTS requires a functional test. Here, we studied the repair efficiency of the two MSH2 missense mutations, L187P and C697F, found in HNPCC families including a few mutation carriers with sebaceous skin tumors. Both mutations were completely deficient in an MMR assay, which together with tumor findings suggested their predisposing role in both internal and skin malignancies in the families.