Single Molecule Molecular Inversion Probes Research Articles

Development, validation and application of single molecule molecular inversion probe based novel integrated genetic screening method for 29 common lysosomal storage disorders in India

BackgroundCurrent clinical diagnosis pathway for lysosomal storage disorders (LSDs) involves sequential biochemical enzymatic tests followed by DNA sequencing, which is iterative, has low diagnostic yield and is costly due to overlapping clinical presentations. Here, we describe a novel low-cost and high-throughput sequencing assay using single-molecule molecular inversion probes (smMIPs) to screen for causative single nucleotide variants (SNVs) and copy number variants (CNVs) in genes associated with 29 common LSDs in India.Results903 smMIPs were designed to target exon and exon–intron boundaries of targeted genes (n = 23; 53.7 kb of the human genome) and were equimolarly pooled to create a sequencing library. After extensive validation in a cohort of 50 patients, we screened 300 patients with either biochemical diagnosis (n = 187) or clinical suspicion (n = 113) of LSDs. A diagnostic yield of 83.4% was observed in patients with prior biochemical diagnosis of LSD. Furthermore, diagnostic yield of 73.9% (n = 54/73) was observed in patients with high clinical suspicion of LSD in contrast with 2.4% (n = 1/40) in patients with low clinical suspicion of LSD. In addition to detecting SNVs, the assay could detect single and multi-exon copy number variants with high confidence. Critically, Niemann-Pick disease type C and neuronal ceroid lipofuscinosis-6 diseases for which biochemical testing is unavailable, could be diagnosed using our assay. Lastly, we observed a non-inferior performance of the assay in DNA extracted from dried blood spots in comparison with whole blood.ConclusionWe developed a flexible and scalable assay to reliably detect genetic causes of 29 common LSDs in India. The assay consolidates the detection of multiple variant types in multiple sample types while having improved diagnostic yield at same or lower cost compared to current clinical paradigm.

Next-generation sequencing to genetically diagnose a diverse range of inherited eye disorders in 15 consanguineous families from Pakistan.

Inherited retinal dystrophies (IRDs) are characterized by photoreceptor dysfunction or degeneration. Clinical and phenotypic overlap between IRDs makes the genetic diagnosis very challenging and comprehensive genomic approaches for accurate diagnosis are frequently required. While there are previous studies on IRDs in Pakistan, causative genes and variants are still unknown for a significant portion of patients. Therefore, there is a need to expand the knowledge of the genetic spectrum of IRDs in Pakistan. Here, we recruited 52 affected and 53 normal individuals from 15 consanguineous Pakistani families presenting non-syndromic and syndromic forms of IRDs. We employed single molecule Molecular Inversion Probes (smMIPs) based panel sequencing and whole genome sequencing to identify the probable disease-causing variants in these families. Using this approach, we obtained a 93% genetic solve rate and identified 16 (likely) causative variants in 14 families, of which seven novel variants were identified in ATOH7, COL18A1, MERTK, NDP, PROM1, PRPF8 and USH2A while nine recurrent variants were identified in CNGA3, CNGB1, HGSNAT, NMNAT1, SIX6 and TULP1. The novel MERTK variant and one recurrent TULP1 variant explained the intra-familial locus heterogeneity in one of the screened families while two recurrent CNGA3 variants explained compound heterozygosity in another family. The identification of variants in known disease-associated genes emphasizes the utilization of time and cost-effective screening approaches for rapid diagnosis. The timely genetic diagnosis will not only identify any associated systemic issues in case of syndromic IRDs, but will also aid in the acceleration of personalized medicine for patients affected with IRDs.

Significance of Microsatellite Instability in Colorectal Carcinoma- A Complete Review

The microsatellite instability (MSI-H) or mismatch repair deficient (dMMR) colorectal tumors recently have been reported that can benefit from immunotherapy, and MSI can be used as a genetic instability of a tumor detection index. Many studies have shown that there are many heterogeneous phenomena in patients with MSI tumors in terms of immunotherapy, prognosis and chemotherapy sensitivity. Here we mainly review the research results of MSI detection methods, its mechanisms, occurrence and its relationship with related tumors, aiming in such a way for brief analysis of the micro satellite instability. Microsatellites (MS) are the repeated sequences of DNA that play an important role in maintaining the tissue morphology. Any mutation of the DNA or chromosomes, lead to the instability of the microsatellites, thereby causing the microsatellite instability. There are three types of microsatellite instability (MSI). High microsatellite instability (MSI-H), low microsatellite instability (MSI-L) and microsatellite stability (MSS). Recent clinical research tends to classify MSS-L and MSS as similar. Microstaellite instability plays an important role in colorectal carcinoma. Based on different molecular mechanisms, MSI in colorectal cancer can be divided into colorectal cancer (CRC) with no obvious family genetic history and Lynch syndrome with non-polyposis with family genetic history. Lynch syndrome is an autosomal dominant disorder and syndrome caused by mutations in MMR strains, and it can also cause tumors in other parts of the colon and rectum. With the recent development of MSI detection technology and immunosuppressant in tumor therapy, researchers found that MSI-H tumors respond well to immunotherapy. There are several methods to detect the microsatellite instability. 1. Next Generation sequencing (NGS), 2. Fluoresence multiplex PCR and capillary electrophoresis. 3. Immunohistochemistry. 4. Single molecule- molecular inversion probes (SmMIP). The main mechanism of MSI includes, Slipped strand mispairing, MMR deficient.

Towards Uncovering the Role of Incomplete Penetrance in Maculopathies through Sequencing of 105 Disease-Associated Genes.

Inherited macular dystrophies (iMDs) are a group of genetic disorders, which affect the central region of the retina. To investigate the genetic basis of iMDs, we used single-molecule Molecular Inversion Probes to sequence 105 maculopathy-associated genes in 1352 patients diagnosed with iMDs. Within this cohort, 39.8% of patients were considered genetically explained by 460 different variants in 49 distinct genes of which 73 were novel variants, with some affecting splicing. The top five most frequent causative genes were ABCA4 (37.2%), PRPH2 (6.7%), CDHR1 (6.1%), PROM1 (4.3%) and RP1L1 (3.1%). Interestingly, variants with incomplete penetrance were revealed in almost one-third of patients considered solved (28.1%), and therefore, a proportion of patients may not be explained solely by the variants reported. This includes eight previously reported variants with incomplete penetrance in addition to CDHR1:c.783G>A and CNGB3:c.1208G>A. Notably, segregation analysis was not routinely performed for variant phasing-a limitation, which may also impact the overall diagnostic yield. The relatively high proportion of probands without any putative causal variant (60.2%) highlights the need to explore variants with incomplete penetrance, the potential modifiers of disease and the genetic overlap between iMDs and age-related macular degeneration. Our results provide valuable insights into the genetic landscape of iMDs and warrant future exploration to determine the involvement of other maculopathy genes.

Clonal hematopoiesis is associated with cardiovascular events in patients with stable coronary artery disease

Clonal hematopoiesis (CH) is a risk factor for atherosclerotic cardiovascular disease, but the impact of smaller clones and the effect on inflammatory parameters is largely unknown. Using ultrasensitive single-molecule molecular inversion probe sequencing, we evaluated the association between CH and a first major adverse cardiovascular event (MACE) in patients with angiographically documented stable coronary artery disease (CAD) and no history of acute ischemic events. CH was associated with an increased rate of MACE at four years follow-up. The size of the clone predicted MACE at an optimal cut-off value of 1.07% variant allele frequency (VAF). Mutation carriers had no change in monocytes subsets or cytokine production capacity but had higher levels of circulating tissue factor, matrilysin, and proteinase-activated receptor-1. Our study identified CH driver mutations with a VAF as small as 1.07% as a residual cardiovascular risk factor and identified potential biomarkers and therapeutic targets for patients with stable CAD.

Mutations in myeloid transcription factors and activated signaling genes predict chronic myeloid leukemia outcomes

AbstractAdvancements in genomics are transforming the clinical management of chronic myeloid leukemia (CML) toward precision medicine. The impact of somatic mutations on treatment outcomes is still under debate. We studied the association of somatic mutations in epigenetic modifier genes and activated signaling/myeloid transcription factors (AS/MTFs) with disease progression and treatment failure in patients with CML after tyrosine kinase inhibitor (TKI) therapy. A total of 394 CML samples were sequenced, including 254 samples collected at initial diagnosis and 140 samples taken during follow-up. Single-molecule molecular inversion probe (smMIP)–based next-generation sequencing (NGS) was conducted targeting recurrently mutated loci in 40 genes, with a limit of detection of 0.2%. Seventy mutations were detected in 57 diagnostic samples (22.4%), whereas 64 mutations were detected in 39 of the follow-up samples (27.9%). Carrying any mutation at initial diagnosis was associated with worse outcomes after TKI therapy, particularly in AS/MTF genes. Patients having these mutations at initial diagnosis and treated with imatinib showed higher risks of treatment failure (hazard ratio, 2.53; 95% confidence interval, 1.13-5.66; P = .0239). The adverse prognostic impact of the mutations was not clear for patients treated with second-generation TKIs. The multivariate analysis affirmed that mutations in AS/MTF genes independently serve as adverse prognostic factors for molecular response, failure-free survival, and progression risk. Additionally, there was an observable nonsignificant trend indicating a heightened risk of progression to advanced disease and worse overall survival. In conclusion, mutations in the AS/MTF genes using smMIP-based NGS can help identify patients with a potential risk of both treatment failure and progression and may help upfront TKI selection.

Cost‐effective smMIPs‐based sequencing to provide a genetic diagnosis for patients with retinitis pigmentosa, Leber congenital amaurosis and macular diseases

Obtaining a genetic diagnosis for IRDs is challenging as more than 280 genes are associated with these conditions. Next‐generation sequencing approaches such as whole exome and genome sequencing are often used but their costs and required infrastructure still prohibit global applicability. Previous studies have shown the cost‐effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Recently, we have developed two smMIPs based panels, one panel to target all genes known to cause retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA), and one panel to target all genes associated with macular diseases (MD). The RP‐LCA and MD panels were used to sequence 4381 and 1352 genetically unsolved probands, respectively. During this lecture, we will discuss the results and effectiveness of our smMIPs based sequencing efforts and highlight some of the novel genotype–phenotype correlations that were identified using these large cohorts.

Chronic TNF in the Aging Microenvironment Exacerbates TET2-loss-of-Function Myeloid Expansion

Introduction: Age-associated TET2 somatic mutations impart an intrinsic hematopoietic stem cell (HSC) advantage and contribute to the phenomenon of clonal hematopoiesis of indeterminate potential (CHIP). Individuals with TET2-mutantCHIP have a higher risk of developing myeloid neoplasms and other age-related conditions, including heart, lung, liver, kidney and infectious disease, and have increased risk of all-cause mortality. Despite its role in unhealthy aging, the extrinsic mechanisms driving TET2-mutant CHIP clonal expansion remain unclear. We previously showed an environment containing TNF favours TET2-mutant HSC expansion in vitro. We therefore postulated that age-related increases in TNF also provide an advantage to HSC and progeny with TET2-mutations in vivo. Methods: All human and mouse studies met ethics approval. C57Bl/6 background wildtype (WT), TNF-α knockout ( TNF-/-), Tet2 hematopoietic knockout (Vav1-iCre-mediated; Tet2-/-) and floxed control mice ( Tet2f/f) mice were obtained from the Jackson Laboratory. Young (6-mo [n=9]) and old (18-22 mo [n=9]) WT mice, and old TNF-/- mice (n=7) were subjected to nonirradiative myeloablation with busulfan, and retro-orbital injections of 8x10 6 cells/ml T-cell-depleted bone marrow (BM), equally harvested from 4-mo-old WT CD45.1 (n=5) and Tet2-/- CD45.2 donor mice (n=5). Flow cytometry was used to confirm and monitor engraftment. Mice were harvested 8 weeks post-transplant for analysis of HSC, progenitor, monocyte and neutrophil populations, and cytokine analyses. Consenting human research participants diagnosed with rheumatoid arthritis (RA) were recruited from the Greater Hamilton Area (Ontario, Canada) from 2016-2018. Blood draws occurred prior to any immunomodulatory treatment (baseline), and at 3- and 6-months following treatment with Adalimumab (Humira®), an anti-TNF agent. CHIP status was determined with our successful 48-gene, targeted, Ion-Torrent based sequencing approach to isolated genomic DNA from PBMC. Confirmation of calls and increased sensitivity to detect clones with VAF < 0.02 employed our established single molecule molecular inversion probes (smMIP)-targeted genomic capture technique and high-depth (47,500X avg. coverage) paired-end sequencing, employing high-stringency filters for error-suppression. Statistical analyses were performed in GraphPad Prism V9.2 or R 4.1.2. Results: 1. Mixed BM chimeric mice of WT and TNF -/- genotypes reconstituted with WT CD45.1 + and Tet2 -/- CD45.2 + HSC showed that age-associated increases in TNF significantly increased by 2- to 2.5-fold the proportions of HSC in old recipient mice, with myeloid lineage skewing (2- to 2.5-fold more granulocyte-monocyte, monocyte-dendritic and common monocyte progenitor cells in BM, and dramatic expansion of Tet2-/- monocytes and neutrophils in blood). This aberrant myelomonocytic advantage was mitigated in old TNF -/- recipient mice, suggesting that TNF signalling in the BM is essential for Tet2-mutant myeloid expansion. 2. Age-associated TNF predisposed Tet2 -/- HSC to the development of Ly6C high inflammatory monocytes, including increased intracellular and serum TNF levels, further exacerbating an inflammatory environment in favor of Tet2-mutantexpansion. 3. Examination of human RA patients (n=7; avg. age 57y) with serial PBMC sampling revealed one patient with CHIP driven by CBL and PPM1D variants, with a 32% reduction in clone size between 3 and 6 months of anti-TNF therapy (adalimumab). Two additional variants were detected at baseline in this RA patient, TP53 R196* (VAF = 1.34%) and ASXL1 P689L (VAF = 3.13%), but these were not detected at 3- and 6-months post-treatment even with high-depth, error suppression sequencing. Two additional patients had detectible low-level CH clones prior to anti-TNF treatment - one with a STAG2 R1033Q variant at baseline (VAF = 1.65%) and the other with a TET2 baseline E798K variant (VAF = 1.68%) - but not detected during anti-TNF treatment. Conclusions: We present novel findings that TNF in the aging BM environment has a causal role in driving TET2-mutant CHIP in vivo, and the first examination of the impact of TNF blockade on CH dynamics in humans, suggesting promise for reducing clonal burden. Larger, prospective studies are required to confirm these findings and to determine if inflammatory cytokine blockade may improve CHIP-comorbid conditions and myeloid cancer risk.

The Presence of Somatic Mutation in Donor Does Not Affect Long-Term Outcomes in 339 Patients Following Allogeneic Hematopoietic Stem Cell Transplantation Using Uniform Fludarabine/Busulfan Myeloablative Conditioning and Cyclosporine/Methotrexate and ATG Gvhd Prophylaxis

Introduction: Clonal hematopoiesis with indeterminate potential (CHIP) constitutes a part of the biological aging process and comprises the acquisition of somatic mutations in hematopoietic stem cells (HSCs). In the context of allogeneic hematopoietic stem cell transplantation (HCT), the potential transfer of CHIP from donor to recipient may raise concerns on HCT-related complications. There are contradictory data on donor CHIP's impact on long-term transplant outcomes using very diverse conditioning regimen as well as various graft-versus-host disease (GVHD) prophylaxis. This study aims to evaluate the impact of donor CHIP on allogeneic HCT outcomes in a cohort of the patients transplanted using a uniform, myeloablative intensity conditioning of Fludarabine-Busulfan (4 days) as well as Cyclosporine/Methotrexate with 4.5 mg/kg rabbit antithymocyte globulin (ATG) over 3 days for GVHD prophylaxis. Patients and methods: Peripheral blood samples were obtained from recipients and their corresponding donors who underwent allogeneic HCT at Tom Baker Cancer Centre, Calgary, Canada. Samples were archived from 339 patients and 255 donors prior to HCT, and additional patient sampling was done on day 28 (D28), day 56 (D56), or day 84 post allogeneic HCT (D84). As a result, paired recipient-donor samples were available for 255 HCTs. This study was approved by the institutional review boards of Princess Margaret Cancer Centre, Toronto, and Tom Baker Cancer Centre, Calgary. For the detection of CHIP, we have applied a bar-coded error-corrected sequencing protocol, a single-molecule molecular inversion probe capture protocol (NAR Genom Bioinform, 2022), which was performed at Wiesmann Institute of Science (Rehovot, Israel). We designed probes targeting 34 genes covering CHIP mutations along with other AML related mutations. Bar-coded NGS library was generated and processed. All statistical analyses were performed using R statistical software 3.5.0 and EZR version 1.41. Results: Sixty-seven clonal mutations in 56 recipients (18.2%) and 22 clonal mutations in 18 donors (7.1%) were detected prior to HCT. For recipients, TET2, JAK2, RUNX1, PPM1D, and DNMT3A were detected in at least 2 patients or more. For donors, the most frequently mutated gene was TET2 (3.1%), and the seconds were DNMT3A and PTPN11 (1.2% for both). Baseline characteristics of 255 patient-donor pairs did not show any difference between D-CHIP and no D-CHIP groups except donor age. Donor CHIP status was distributed evenly throughout most of the demographics of recipients, type of disease, pre-transplant status, and transplant procedure. Most of the pts received peripheral blood stem cells (97%). With a median follow up duration 6.02 years, the 5-year OS rates tend to be higher in no D-CHIP group than D-CHIP group (63.1% vs 42.8%) with a HR of 1.73 (95% CI [0.90-3.35]), although it was not statistically significant (p=0.096). The cumulative incidence of relapse for both groups were not different in 5 years (28.1% vs. 28.4%, p=0.849). The cumulative incidence of NRM within 5 years in D-CHIP group was slightly higher than no D-CHIP group (28.4% vs 17.5%), but it was not statistically significant (p=0.250). Neutrophil engraftment by day 28 was 99.1% vs. 100%, without statistical difference between the two groups (p=0.785). The cumulative incidence of grade II-IV acute GVHD within day+100 seemed to be higher in D-CHIP group compared to no D-CHIP group, but it was not statistically significant (24.8% vs. 34.5%, p=0.148; Figure A). In terms of chronic GVHD, cumulative incidence of moderate to severe GVHD was significantly higher in 5 years after transplant (29.4% vs. 58.8%; HR 2.55 [1.331-4.96], p=0.006; Figure B). Even when we set the cut off level of donor CHIP positivity up to >1% or >10%, the association between donor CHIP and risk of chronic GVHD remained significant. The impact of donor CHIP on the cumulative incidence of moderate to severe GVHD was confirmed in multivariate analysis (HR 2.3 [1.3-4.1], p=0.003). Other factors associated with moderate to severe chronic GVHD were previous history of grade II-IV acute GVHD (p=0.008) and donor type (p=0.054). Conclusion: Under clinical setting of uniform conditioning regimen and GVHD prophylaxis incorporating ATG (4.5mg/kg), donor CHIP was found to be associated with higher risk of moderate to severe chronic GVHD, while it does not affect other allogeneic HCT outcomes.

A Novel and Cost-Efficient Measurable Residual Disease (MRD) Detection Assay Using a Single Molecule Molecular Inversion Probe-Based Next Generation Sequencing (NGS) Assay Predicts Overall Survival in Patients with Acute Myeloid Leukemia Undergoing Allogeneic Stem Cell Transplantation

Introduction Relapse remains the main reason for poor outcomes of patients (pts) with acute myeloid leukemia (AML). Allogeneic hematopoietic stem cell transplantation (HSCT) is the preferred post-remission treatment in pts at high risk of relapse. The presence of measurable residual disease (MRD) after intensive frontline treatment or before or after HSCT has emerged as an important predictor of relapse. Various methods are used for MRD detection, including flow cytometry and molecular assays detecting individual gene mutations (mut) such as NPM1mut. Next generation sequencing (NGS)-based assays covering multiple genes commonly mutated in AML may allow sensitive MRD detection in a broad range of pts with diverse genetic characteristics. Methods We established a targeted, error corrected NGS MRD assay utilizing single-molecule molecular inversion probes (smMIPs). The smMIP protocol uses a hybridization-capture approach to selectively enrich and amplify both DNA strands of 92 regions in 32 genes in a single reaction. Unique molecular identifiers (UMIs) facilitate computational correction of sequencing errors to enable reliable detection of variants ≥0.5% variant allele frequency (VAF), with the additional advantage of relatively low reagent and sequencing costs of < $100 per sample. The smMIP assay was used to evaluate MRD status on pre-HSCT bone marrow samples from 98 AML pts who received an HSCT in first (n=83) or second (n=15) complete remission with or without count recovery. Median age at HSCT was 59 (range 20-75) years, 42% were female; 70% had de novo AML, 19% had an antecedent myeloid neoplasm and 11% had AML post cytotoxic therapy. European LeukemiaNet (ELN)-2022 risk groups at diagnosis were favorable in 11%, intermediate in 33%, adverse in 20% and unknown in 22%. All pts had received intensive induction chemotherapy. Twenty-nine percent received a myeloablative conditioning regimen (MAC), while 23% received reduced intensity conditioning (RIC) and 48% a non-myeloablative (NMA) conditioning regimen. Donors were matched related (18%), haploidentical (6%), or matched (55%) or mismatched (21%) unrelated. The median follow-up for pts alive was 34.8 months. Results Overall, we detected 190 variants in 71 (72%) of 98 pre-HSCT remission samples. The most commonly affected genes were DNMT3A (in 37% of pts), TET2 (21%), PPM1D (12%), IDH2 (10%) and TP53 (5%). Twenty-nine percent of pts had only variants affecting the clonal hematopoiesis-related genes DNMT3A, TET2 or ASXL1 (‘DTA‘), while 44% of patients had ≥1 variant involving a non-DTA gene. MRD-positive pts, defined as those with ≥1 non-DTA variant, had similar baseline and HSCT-related characteristics (includingage, sex, ELN risk group, de novo vs. secondary AML) compared to pts without non-DTA variants. Overall survival (OS) was significantly inferior in NGS MRD-positive pts compared to those with no non-DTA variant (Figure A, 5-year OS, 49% vs. 85%, P=.011). MRD-positive pts also had a non-significant higher cumulative incidence of relapse at 5 years (46% vs. 24%, P=.14), while non-relapse mortality was similar in both groups (P=.72). We next performed multivariable analyses, considering variables associated with OS at an univariable P<.10 (MRD status, patient sex, therapy-related AML, conditioning intensity), and using stepwise backward variable selection to identify factors significantly associated with OS (Figure B). In the final multivariable model, pre-HSCT MRD detection remained associated with inferior OS (hazard ratio 2.51; 95% confidence interval, 1.07 - 5.91; P=.035). Female sex associated with favorable OS, while myeloablative conditioning (MAC) showed a borderline significant association with superior OS. Of note, we did not detect an interaction between conditioning intensity and detection of MRD with regard to OS, i.e. the prognostic association of MRD detection was not different between pts receiving myeloablative or less-intensive conditioning. However, this analysis was limited by the small patient number. Conclusion Detection of MRD by targeted NGS using the smMIPs approach provides prognostic information in pts undergoing allogeneic HSCT, including those without established molecular markers such as NPM1mut. This method is applicable to a large proportion of AML pts and is cost-efficient for broad clinical use. S.M.K. and T.H., and M.J. and K.H.M. contributed equally to this abstract.

Characterization of Clonal Hematopoietic of Indeterminate Potential (CHIP) Mutations in an Imid-Naïve Multiple Myeloma (MM) Autologous Stem Cell Transplant (ASCT) Population: First Results from a Pre-Transplant Time Point in a Prospective, Longitudinal Study

Background: Clonal Hematopoiesis of Indeterminate Potential (CHIP) is defined by the acquisition of ≥ 1 somatic mutations in the blood of healthy adults, but can also be detected at higher prevalence in patients with malignancies, particularly after DNA damaging therapy. The presence of CHIP mutations in MM confers a reduced overall survival (Mouhieddine, JCO 2020) but high quality, prospective evaluation of CHIP mutation evolution over the transplant sequence, including the impact of high-dose melphalan and immunomodulatory (IMiD)-based therapy, is largely under-studied. Serial assessment of CHIP over the transplant course has been reported from the coMMpass dataset, demonstrating a 4-fold increase in mutation prevalence from 5.8% at diagnosis to 25% after 3.1 years (Mouhieddine, Blood, 2021). In this data set, most patients were exposed to prior IMiD-containing at some point during therapy. Whether the survival benefit reported with IMiD-based maintenance therapy post-transplant is associated with CHIP mutation modulation is unclear. We are therefore investigating the longitudinal evolution of CHIP in a cohort of transplant-eligible, largely IMiD-naïve patients (pts) over the pre- and post-ASCT course in an ongoing study. Here, we present preliminary findings from the pre-transplant time-point after non-IMiD-containing induction but before high-dose melphalan and ASCT. Methods: The ongoing Princess Margaret Cancer Center ARCH 001 trial is a prospective, longitudinal study evaluating evolution of CHIP in a transplant-eligible MM population. Mutation testing is performed using the highly sensitive single-molecule molecular inversion probe (SmMIP) next-generation sequencing (NGS) technique (Abelson, Bioinformatics, 2022). After sequencing with a minimum sequencing depth of 4000x, the list of mutation calls produced by smMIP-tools is subject to various filters to reduce the likelihood of false positives. Synonymous mutations, as well as any variants falling within introns or splice regions are removed. The minor allele frequency of the variant (if available) is required to be above 0.1% so as to exclude mutations that are common SNPs. VAF frequency threshold of 1-30 % is set for calling somatic mutations, with a view to minimize false positives and germ-line mutations. Multiple time points for testing pertinent to therapy include: within 1 month pre-transplant (after induction and stem cell collection), 3 months post-transplant, and two subsequent samples 12 and 24 months post-sample 2. Here we report preliminary results of CHIP mutation testing in the first 66 pts at the pre-transplant time point. Results: Patient, disease and treatment characteristics for all pts and their stratification by the presence of CHIP mutations are outlined in Table 1. The total cohort is typical for a transplant-eligible population with median age 65 years, male predominance (M 59%/F 41%), 60% IgG subtype, 23% high-risk FISH cytogenetics. Most (90%) received a non-IMiD containing induction regimen CyBorD; only 6% received an IMiD pre-ASCT. CHIP mutations were identified in 28/66 pts, for a mutation prevalence rate of 43%; 6 patients (9%) carried ≥ 1 mutation. The median age at transplant as well as other baseline demographics did not differ between those with and without mutations (Table 1). Mutation profiles are shown in Figure 1, and are consistent with those described in the literature with the most commonly mutated genes being DNMT3a, TET2, ASXL1 and PPM1D, and the mutation prevalence rate highest for DNMT3a at 21%. 6 pts (9%) had ≥ 1 mutation (range 2-3) identified, with 3 of 6 involving the DNMT3a gene. Other genes involved in patients with multiple mutations were TET2 (n=3), ASXL1 (n=2), PPM1D (n=2), SRSF2 (n=1), SF3B1 (n=1). Mean allele frequency was 4%, ranging from 1-19. Conclusion: Our results using deep SmMIP sequencing show a mutation prevalence rate of 43% in a cohort of transplant-eligible, largely IMiD-naive MM pts studied after induction. These rates are higher than those generally described in the literature, which may relate to the high sensitivity of the assay used, variation in filtering between institutions, and the deliberate use of a relatively low VAF threshold with the intent to capture clinically significant variants for longitudinal tracking during the course of this ongoing study. Further studies during lenalidomide maintenance will be forthcoming.

Heterozygous COL17A1 variants are a frequent cause of amelogenesis imperfecta

BackgroundCollagen XVII is most typically associated with human disease when biallelic COL17A1 variants (>230) cause junctional epidermolysis bullosa (JEB), a rare, genetically heterogeneous, mucocutaneous blistering disease with amelogenesis imperfecta (AI),...

Clonal hematopoiesis has prognostic value in dilated cardiomyopathy independent of age and clone size

Abstract Background Clonal hematopoiesis (CH) gives rise to mutated leukocyte clones, that may induce cardiovascular inflammation, and thereby impact the disease course in cardiovascular diseases such as atherosclerosis and ischemic heart failure. The term clonal hematopoiesis of indeterminate potential (CHIP) is used when the variant allele frequency (VAF; a marker for clone size) in blood is ≥2%. The impact of CH clones in non-ischemic dilated cardiomyopathy (DCM) remains largely undetermined. Moreover, the impact of small clone sizes (VAF <0.5%) remains unknown in cardiovascular diseases in general. Objectives To establish the prognostic impact of CH in DCM down to small CH clone sizes. Methods CH was determined using an ultrasensitive single-molecule Molecular Inversion Probe technique that allows detection of clones down to a VAF of 0.01%. Cardiac death and all-cause mortality were predicted using receiver operating characteristic curve-optimized VAF cut-off values. Results 520 DCM patients were included. 109 patients (21%) had CH driver mutations, of which 45 had a VAF of ≥2% and 31 had a VAF of <0.5%. The median follow-up duration was 6.49 years [interquartile range 4.69 - 9.71]. DCM patients with CH had a higher risk of cardiac death (HR 2.33 using a VAF cut-off of 0.36%, 95% confidence interval 1.24 - 4.40) and all-cause mortality(HR 1.72 using a VAF cut-off of 0.06%, 95% confidence interval 1.10 - 2.69), independent of age, sex, left ventricle ejection fraction and New York Heart Association classification. Conclusion CH predicts cardiac death and all-cause mortality in DCM patients with an optimal threshold for clone size of 0.36% and 0.06%, respectively. Therefore, CH may be prognostically relevant independent of clone size in patients with DCM.Clonal hematopoiesis characteristicsClonal hematopoiesis prognosis

Targeted sequencing and in vitro splice assays shed light on ABCA4-associated retinopathies missing heritability

The ABCA4 gene is the most frequently mutated Mendelian retinopathy-associated gene. Biallelic variants lead to a variety of phenotypes, however, for thousands of cases the underlying variants remain unknown. Here, we aim to shed further light on the missing heritability of ABCA4-associated retinopathy by analyzing a large cohort of macular dystrophy probands. A total of 858 probands were collected from 26 centers, of whom 722 carried no or one pathogenic ABCA4 variant while 136 cases carried two ABCA4 alleles, one of which was a frequent mild variant, suggesting that deep-intronic variants (DIVs) or other cis-modifiers might have been missed. After single molecule molecular inversion probes (smMIPs)-based sequencing of the complete 128-kb ABCA4 locus, the effect of putative splice variants was assessed in vitro by midigene splice assays in HEK293T cells. The breakpoints of copy number variants (CNVs) were determined by junction PCR and Sanger sequencing. ABCA4 sequence analysis solved 207/520 (39.8%) naïve or unsolved cases and 70/202 (34.7%) monoallelic cases, while additional causal variants were identified in 54/136 (39.7%) of probands carrying two variants. Seven novel DIVs and six novel non-canonical splice site variants were detected in a total of 35 alleles and characterized, including the c.6283-321C>G variant leading to a complex splicing defect. Additionally, four novel CNVs were identified and characterized in five alleles. These results confirm that smMIPs-based sequencing of the complete ABCA4 gene provides a cost-effective method to genetically solve retinopathy cases and that several rare structural and splice altering defects remain undiscovered in STGD1 cases.

Clonal Hematopoiesis Has Prognostic Value in Dilated Cardiomyopathy Independent of Age and Clone Size

BackgroundClonal hematopoiesis (CH) gives rise to mutated leukocyte clones that induce cardiovascular inflammation and thereby impact the disease course in atherosclerosis and ischemic heart failure. CH of indeterminate potential refers to a variant allele frequency (VAF) (a marker for clone size) in blood of ≥2%. The impact of CH clones—including small clone sizes (VAF <0.5%)—in nonischemic dilated cardiomyopathy (DCM) remains largely undetermined. ObjectivesThe authors sought to establish the prognostic impact of CH in DCM including small clones. MethodsCH is determined using an ultrasensitive single-molecule molecular inversion probe technique that allows detection of clones down to a VAF of 0.01%. Cardiac death and all-cause mortality were analyzed using receiver-operating characteristic curve–optimized VAF cutoff values. ResultsA total of 520 DCM patients have been included. A total of 109 patients (21%) had CH driver mutations, of which 45 had a VAF of ≥2% and 31 <0.5%. The median follow-up duration was 6.5 years (IQR: 4.7-9.7 years). DCM patients with CH have a higher risk of cardiac death (HR: 2.33 using a VAF cutoff of 0.36%, 95% CI: 1.24-4.40) and all-cause mortality (HR: 1.72 using a VAF cutoff of 0.06%, 95% CI: 1.10-2.69), independent of age, sex, left ventricular ejection fraction, and NYHA functional classification. ConclusionsCH predicts cardiac death and all-cause mortality in DCM patients with optimal thresholds for clone size of 0.36% and 0.06%, respectively. Therefore, CH is prognostically relevant, independent of clone size in patients with DCM.

Cost-effective sequence analysis of 113 genes in 1,192 probands with retinitis pigmentosa and Leber congenital amaurosis.

Introduction: Retinitis pigmentosa (RP) and Leber congenital amaurosis (LCA) are two groups of inherited retinal diseases (IRDs) where the rod photoreceptors degenerate followed by the cone photoreceptors of the retina. A genetic diagnosis for IRDs is challenging since >280 genes are associated with these conditions. While whole exome sequencing (WES) is commonly used by diagnostic facilities, the costs and required infrastructure prevent its global applicability. Previous studies have shown the cost-effectiveness of sequence analysis using single molecule Molecular Inversion Probes (smMIPs) in a cohort of patients diagnosed with Stargardt disease and other maculopathies. Methods: Here, we introduce a smMIPs panel that targets the exons and splice sites of all currently known genes associated with RP and LCA, the entire RPE65 gene, known causative deep-intronic variants leading to pseudo-exons, and part of the RP17 region associated with autosomal dominant RP, by using a total of 16,812 smMIPs. The RP-LCA smMIPs panel was used to screen 1,192 probands from an international cohort of predominantly RP and LCA cases. Results and discussion: After genetic analysis, a diagnostic yield of 56% was obtained which is on par with results from WES analysis. The effectiveness and the reduced costs compared to WES renders the RP-LCA smMIPs panel a competitive approach to provide IRD patients with a genetic diagnosis, especially in countries with restricted access to genetic testing.

Effective smMIPs-Based Sequencing of Maculopathy-Associated Genes in Stargardt Disease Cases and Allied Maculopathies from the UK.

Macular dystrophies are a group of individually rare but collectively common inherited retinal dystrophies characterised by central vision loss and loss of visual acuity. Single molecule Molecular Inversion Probes (smMIPs) have proved effective in identifying genetic variants causing macular dystrophy. Here, a previously established smMIPs panel tailored for genes associated with macular diseases has been used to examine 57 UK macular dystrophy cases, achieving a high solve rate of 63.2% (36/57). Among 27 bi-allelic STGD1 cases, only three novel ABCA4 variants were identified, illustrating that the majority of ABCA4 variants in Caucasian STGD1 cases are currently known. We examined cases with ABCA4-associated disease in detail, comparing our results with a previously reported variant grading system, and found this model to be accurate and clinically useful. In this study, we showed that ABCA4-associated disease could be distinguished from other forms of macular dystrophy based on clinical evaluation in the majority of cases (34/36).

Relevance of Molecular Profiling in Patients With Low-Grade Endometrial Cancer

Patients with low-grade (ie, grade 1-2) endometrial cancer (EC) are characterized by their favorable prognosis compared with patients with high-grade (ie, grade 3) EC. With the implementation of molecular profiling, the prognostic relevance of tumor grading might lose attention. As most patients present with low-grade EC and have an excellent outcome, the value of molecular profiling for these patients is unclear. To determine the association of molecular profiling with outcomes among patients with low-grade EC. This retrospective cohort study included a multicenter international European cohort of patients diagnosed with EC between 1994 and 2018, with a median follow-up of 5.9 years. Molecular subgroups were determined by next-generation sequencing using single-molecule molecular inversion probes and by immunohistochemistry. Subsequently, tumors were classified as polymerase epsilon (POLE)-altered, microsatellite instable (MSI), tumor protein p53 (TP53)-altered, or no specific molecular profile (NSMP). Patients diagnosed with any histological subtypes and FIGO (International Federation of Gynecology and Obstetrics) stages of EC were included, but patients with early-stage EC (FIGO I-II) were only included if they had known lymph node status. Data were analyzed February 20 to June 16, 2022. Molecular testing of the 4 molecular subgroups. The main outcome was disease-specific survival (DSS) within the molecular subgroups. A total of 393 patients with EC were included, with a median (range) age of 64.0 (31.0-86.0) years and median (range) body mass index (BMI; calculated as weight in kilograms divided by height in meters squared) of 29.1 (18.0-58.3). Most patients presented with early-stage (290 patients [73.8%]) and low-grade (209 patients [53.2%]) disease. Of all patients, 33 (8.4%) had POLE-altered EC, 78 (19.8%) had MSI EC, 72 (18.3%) had TP53-altered EC, and 210 (53.4%) had NSMP EC. Across all molecular subgroups, patients with low-grade EC had superior 5-year DSS compared with those with high-grade EC, varying between 90% to 100% vs 41% to 90% (P < .001). Multivariable analysis in the entire cohort including age, tumor grade, FIGO stage, lymphovascular space invasion, and the molecular subgroups as covariates found that only high-grade (hazard ratio [HR], 4.29; 95% CI, 2.15-8.53; P < .001), TP53-altered (HR, 1.76; 95% CI, 1.04-2.95; P = .03), and FIGO stage III or IV (HR, 4.26; 95% CI, 2.50-7.26; P < .001) disease were independently associated with reduced DSS. This cohort study found that patients with low-grade EC had an excellent prognosis independent of molecular subgroup. These findings do not support routine molecular profiling in patients with low-grade EC, and they demonstrate the importance of primary diagnostic tumor grading and selective profiling in low-grade EC to increase cost-effectiveness.

Targeted Resequencing of Otosclerosis Patients from Different Populations Replicates Results from a Previous Genome-Wide Association Study.

Otosclerosis is one of the most common causes of hearing loss in young adults. It has a prevalence of 0.3-0.4% in the European population. Clinical symptoms usually occur between the second and fifth decade of life. Different studies have been performed to unravel the genetic architecture of the disease. Recently, a genome-wide association study (GWAS) identified 15 novel risk loci and replicated the regions of three previously reported candidate genes. In this study, seven candidate genes from the GWAS were resequenced using single molecule molecular inversion probes (smMIPs). smMIPs were used to capture the exonic regions and the 3' and 5' untranslated regions (UTR). Discovered variants were tested for association with the disease using single variant and gene-based association analysis. The single variant results showed that 13 significant variants were associated with otosclerosis. Associated variants were found in five of the seven genes studied here, including AHSG, LINC01482, MARK3, SUPT3H and RELN. Conversely, burden testing did not show a major role of rare variants in the disease. In conclusion, this study was able to replicate five out of seven candidate genes reported in the previous GWAS. This association is likely mainly driven by common variants.

Diagnostic accuracy of mutational analysis along the Müllerian tract to detect ovarian cancer

ObjectiveOvarian cancer is known for its poor prognosis, which is mainly due to the lack of early symptoms and adequate screening options. In this study we evaluated whether mutational analysis...