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In a non-negligible number of patients with metastatic colorectal cancer (mCRC), the peritoneum is the predominant site of dissemination. Cure can be achieved by cytoreductive surgery (CRS) and hyperthermic intraperitoneal chemotherapy (HIPEC), but this procedure is associated with long-term morbidity and high relapse rates. Thus, there is a pressing need for improved therapeutic strategies and complementary biomarkers. The present study explored the molecular heterogeneity in mCRC with peritoneal carcinomatosis (PC), and the potential clinical implications thereof. Multi-region immunohistochemical profiling and deep targeted DNA-sequencing was performed on chemotherapy-naïve tumours from seven patients with synchronous colorectal PC who underwent CRS and HIPEC. In total, 88 samples (5-19 per patient) were analysed, representing primary tumour, lymph node metastases, tumour deposits, PC and liver metastases. Expression of special AT-rich sequence-binding protein 2 (SATB2), a marker of colorectal lineage, was lacking in the majority of cases, and a conspicuous intra-patient heterogeneity was denoted for expression of the proposed prognostic and predictive biomarker RNA-binding motif protein 3 (RBM3). Loss of mismatch repair proteins MLH1 and PSM2, observed in one case, was concordant with microsatellite instability and the highest tumour mutational burden. When present in a patient, mutations in key CRC driver genes, i.e., KRAS, APC and TP53, were homogenously distributed across all samples, while less common mutations were more heterogenous. On the same note, copy number variations showed intra-patient as well inter-patient heterogeneity. In two out of seven cases, hierarchical clustering revealed that samples from the PC and lymph node metastases were more similar to each other than to the primary tumour. In summary, these findings should encourage additional studies addressing the potential distinctiveness of mCRC with PC, which might pave the way for improved personalized treatment of these patients.

Purpose: While patients with intermediate-risk Wilms tumors (WT) now have an overall survival rate of almost 90%, those affected by high-stage tumors with diffuse anaplasia (DA) have an overall survival of only around 50%. We here identify key events in the pathogenesis of DA by mapping cancer cell evolution over anatomic space in WTs. Experimental Design: We spatially mapped subclonal landscapes in a retrospective cohort of 20 WTs using high-resolution copy number profiling and TP53 mutation analysis followed by clonal deconvolution and phylogenetic reconstruction. Tumor whole mount sections were utilized to characterize the distribution of subclones across anatomically distinct tumor compartments. Results: Compared to non-DA WTs, tumors with DA showed a significantly higher number of genetically distinct tumor cell subpopulations and more complex phylogenetic trees, including high levels of phylogenetic species richness, divergence and irregularity. All regions with classical anaplasia showed TP53 alterations. TP53 mutations were frequently followed by saltatory evolution and parallel loss of the remaining wild-type allele in different regions. Morphological features of anaplasia increased with copy number aberration (CNA) burden and regressive features. Compartments demarcated by fibrous septae or necrosis/regression were frequently (73%) associated with the emergence of new clonal CNAs, while clonal sweeps were rare within these compartments. Conclusions: WTs with DA display significantly more complex phylogenies compared to non-DA WTs, including features of saltatory and parallel evolution. The subclonal landscape of individual tumors was constrained by anatomic compartments, which should be considered when sampling tissue for precision diagnostics.

Supplementary Data from Branching Copy-Number Evolution and Parallel Immune Profiles across the Regional Tumor Space of Resected Pancreatic Cancer

Neuroblastoma (NB) is one of the most lethal childhood cancers due its propensity to treatment resistance. By spatial mapping of subclone geographies before and after chemotherapy across 89 tumor regions from 12 NBs, we find that densely packed territories of closely related subclones present at diagnosis are replaced under effective treatment by islands of distantly related survivor subclones, originating from a different most recent ancestor compared to lineages dominating before treatment. Conversely, in tumors that progressed under treatment, ancestors of subclones dominating later in disease are present already at diagnosis. Chemotherapy treated xenografts and cell culture models replicates these two contrasting scenarios and shows branching evolution to be a constant feature of proliferating NB cells. Phylogenies based on whole genome sequencing of 505 individual NB cells indicate that a rich repertoire of parallel subclones, emerges already with the first oncogenic mutations and lays the foundation for clonal replacement under treatment.

Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers and high-risk adult cancer. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on data from 56 pediatric tumors comprising 253 tumor biopsies and show a robust performance on simulations of bulk genotyping data. We also benchmark DEVOLUTION to similar bioinformatic tools using an external dataset. DEVOLUTION holds the potential to facilitate insights into the development, progression, and response to treatment, particularly in tumors with high burden of chromosomal copy number alterations., Natalie Andersson et al. present DEVOLUTION, an algorithm and tool that allows researchers to reconstruct tumor clonal lineages from copy number and/or sequencing data. They validate this method on a diverse cohort of pediatric cancers, demonstrating its potential applications for cancer research.

Despite the advent of personalized medicine, it is still difficult to predict how a cancer develops over time at the level of the individual patient or even in cancer model systems which begs the question whether certain aspects of cancer can ever be predicted or if there is an inherent unpredictability in cancer, similar to other complex biological systems, We demonstrate by a combination of agent-based mathematical modelling and analysis of data from patient-derived xenograft systems from multiple cancer types that certain conditions may invoke chaotic fluctuations in the clonal landscape of cancer cells. Our findings indicate that under those conditions, the cancer genome behaves as a complex dynamic system, making its long-term evolution inherently unpredictable.

BackgroundObservational studies regarding the correlation between the use of antihypertensive medication and the risk of breast cancer (BC) reported inconsistent findings. We performed a two-sample Mendelian randomization using instrumental variables to proxy changes in gene expressions of antihypertensive medication targets to interrogate this.MethodsWe assessed the association between single-nucleotide polymorphisms (SNPs) and drug targetable gene expression with expression quantitative trait loci in blood. Further, we investigated association between the SNPs and BC risk with genome-wide association study summary statistics. We then confirmed the hits from Mendelian randomization with tissue-specific analyses along with additional sensitivity assessments (horizontal pleiotropy, colocalization, multiple tissue enrichment etc.).ResultsThe overall BC risk was decreased 16% with one standard deviation (SD) increase of SLC12A2 gene expression in blood (odds ratio, 0.86, 95% confidential interval, 0.78-0.94). This signal was further confirmed in estrogen receptor positive (ER+) BC (0.85, 0.78-0.94). In addition, one SD increase in expression of PDE1B in blood was associated with 7% increased risk of ER+ BC (1.07, 1.03-1.11). We detected no evidence of horizontal pleiotropy for these associations and the probability of the causal variants being shared between the gene expression and BC risk was 81.5%, 40.5% and 66.8%, respectively. We failed to observe any significant association between other targeted genes and BC risk.ConclusionsUse of antihypertensive medications that target SLC12A2 and PDE1B is associated with increased and decreased BC risk, respectively.FundingThis work was supported by the Swedish Research Council [2018-02400 to K.S., 2020-01175 to J.S., 2021-01187 to J.J.], Cancerfonden [2017 CAN2017/340 to J.J.], Crafoordska Stiftelsen [to J.J.], MAS Cancer [to J.J.], ALF funding from Region Skåne [to J.J. and K.S.]. The funding body was not involved in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Background: Survival in malignant cutaneous melanoma has improved but increasing survival will result in an increased likelihood of the occurrence of second primary cancers (SPCs). SPCs may adversely interfere with survival. We quantified survival in patients with different types of SPCs, in comparison to known poor prognostic indicators of metastatic disease. Methods: Data for melanoma and any SPCs were obtained from the Swedish Cancer Registry for years 2003 through 2015, including clinical TNM classification. SPCs were grouped into three ‘prognostic groups’ based on 5-year relative survival of these cancers as first primary cancer. Kaplan-Meier survival curves were generated and hazard ratios were estimated using Cox regression, adjusted for a number of variables and treating diagnosis of SPC as a time-dependent variable. Results: The total number of first melanoma patients was 28,716 followed by 3,202 (11.1%) SPCs, 1/3 of which had a second melanoma while 2/3 had other SPCs. Among men diagnosed at age over 70 years, who survived at least 10 years, 31.4% had SPC. HRs (95% CI) for survival increased systematically from the reference rate of 1.00 (no SPC) to 1.59 (1.35–1.87) with SPC of good prognosis (78.6% of SPCs) to 3.49 (2.58–4.72) of moderate prognosis (12.0%) and to 7.93 (5.50–11.44) of poor prognosis (9.4%). In patients without SPC, the HRs increased to 2.62 (2.02–3.39) with any nodal metastases and to 5.88 (4.57–7.57) with any distant metastases compared to patients without local or distant metastases. Conclusion: The data showed that SPCs are an increasingly common negative prognostic factor for melanoma. Future attempts to improve melanoma survival need to target SPCs. (Less)

Pancreatic ductal adenocarcinoma (PDAC) remains a highly lethal disease. The only option for curative treatment is resection of the tumor followed by standard adjuvant chemotherapy. Yet, early relapse due to chemoresistance is almost inevitable. Herein, we delineated the genetic intratumor heterogeneity in resected PDAC, with the aim to identify evolutionary patterns that may be associated with overall survival (OS) following treatment with curative intent. Potential relationships with the adjacent immune microenvironment were also examined. The genetic and immune landscapes of the regional tumor space were analyzed in nine patients with resected PDAC. Targeted deep sequencing and genome wide SNP array were followed by clonal deconvolution and phylogenetic analysis. A mathematical complexity score was developed to calculate the network extent of each phylogeny. Spatial variation in abundancy and tumor nest infiltration of immune cells was analyzed by double IHC staining. Copy-number heterogeneity was denoted as the major contributing factor to the branching architectures of the produced phylogenetic trees. Increased tree complexity was significantly inversely associated with OS, and larger regional maximum aberrations (higher treetops) were associated with increased PD-L1 expression on tumor cells. Contrastingly, an FREM1 gene amplification, found in one patient, coincided with a particularly vigorous immune response. Findings from this limited case series suggest that complex evolutionary patterns may be associated with a shorter survival in surgically treated patients with PDAC. Some hypothesis-generating associations with the surrounding immune microenvironment were also detected.Evolutionary copy-number patterns may be associated with survival in patients with resected PDAC.

Second primary cancers (SPCs) account for an increasing proportion of all cancer diagnoses and family history of cancer may be a risk factor for SPCs. Using the Swedish Family-Cancer Database on non-Hodgkin lymphoma (NHL), we assessed the influence of family history on risk of SPCs and of SPCs on survival. NHL patients were identified from the years 1958 to 2015 and generalized Poisson models were used to calculate relative risks (RRs) for SPCs and familial SPCs. Among 14,393 NHL patients, a total of 1,866 (13.0%) were diagnosed with SPC. Familial risk of nine particular cancers were associated with risks of these cancers as SPCs, with 2 to 5-fold increases in RRs. At the end of a 25-year follow-up period, the survival probability for persons with SPC was only 20% of that for patients without SPC; the hazard ratio for SPC was 1.59 (95% CI: 1.46 ? 1.72). Survival could be predicted by the prognostic groups based on first cancers and HRs increase systematically with worse prognosis yielding a trend of P = 4.6x10-5. SPCs had deleterious consequences for survival in NHL patients. Family history was associated with increasing numbers of SPCs. Prevention of SPCs and their early detection is an important target in the overall strategy to improve survival in NHL patients. Counseling for avoidance of risk factors and targeted screening based on family history are feasible steps in risk reduction. This article is protected by copyright. All rights reserved.

Inherited genetic susceptibility to multiple myeloma has been investigated in a number of studies. Although 23 individual risk loci have been identified, much of the genetic heritability remains unknown. Here we carried out genome-wide interaction analyses on two European cohorts accounting for 3,999 cases and 7,266 controls and characterized genetic susceptibility to multiple myeloma with subsequent meta-analysis that discovered 16 unique interacting loci. These risk loci along with previously known variants explain 17% of the heritability in liability scale. The genes associated with the interacting loci were found to be enriched in transforming growth factor beta signaling and circadian rhythm regulation pathways suggesting immunoglobulin trait modulation, TH17 cell differentiation and bone morphogenesis as mechanistic links between the predisposition markers and intrinsic multiple myeloma biology. Further tissue/cell-type enrichment analysis associated the discovered genes with hemic-immune system tissue types and immune-related cell types indicating overall involvement in immune response., Subhayan Chattopadhyay et al. conduct genome-wide interaction studies to identify genetic susceptibility to multiple myeloma. They find 16 unique interacting loci, which implicate immune response in multiple myeloma pathology.

To assess etiological and clinical consequences of second primary cancers (SPCs) in prostate cancer (PC) patients, we followed newly diagnosed patients to identify men who were diagnosed with a SPC and recorded their causes of death. We used the Swedish Family-Cancer Database to assess relative risks (RRs) and causes of death in SPCs until the year 2015 in patients with a PC diagnosis between 2001 and 2010. Among a total of 4.26 million men, 76 614 were diagnosed with PC at the median age of 71 years. Among them, 8659 (11.3%) received a subsequent diagnosis of SPC after a median follow-up of 4 years. The most common SPCs were colorectal, skin, bladder, and lung cancers, melanoma, and non-Hodgkin lymphoma. The ranking was almost identical with first cancers among elderly men in Sweden. The RR for SPCs in prostate-specific antigen-detected PC was approximately equal to RR in other PC. Mortality patterns of PC patients were distinct depending on the presence or absence of SPC. Among patients with SPC, 47.8% died as a result of the corresponding SPC, followed by other causes (22.2%) and PC (18.1%). For patients without SPC, PC and non-neoplastic causes almost matched each other as the main causes of death (48.5% and 47.8%). The results suggest that SPCs appear autonomous from primary PC and reflect incidence and mortality of first cancers in general. SPC was the most common cause of death in patients with SPC; close to half of the patients died due to SPC. For improved survival in PC patients, prevention and early detection of SPCs would be important, and the present results suggest that risk factors for SPC in PC are the same as those for first cancer in general.

Guoqiao Zheng,1,2 Subhayan Chattopadhyay,1,2 Asta Försti,1,3 Kristina Sundquist,3–6 Kari Hemminki1,3 1Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Baden-Württemberg, Germany; 2Faculty of Medicine, University of Heidelberg, Heidelberg, Baden-Württemberg, Germany; 3Center for Primary Health Care Research, Lund University, 205 02 Malmö, Skåne County, Sweden; 4Department of Family Medicine and Community Health, 5Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 6Center for Community-Based Healthcare Research and Education (CoHRE), Department of Functional Pathology, School of Medicine, Shimane University, Izumo, Japan Background: With improving survival in ovarian cancer, second primary cancers (SPCs) and their etiological foundations are becoming an issue. The ways in which family history may influence the occurrence of SPCs and the related mortality are not well known. Methods: Based on the Swedish Family-Cancer Database, we identified 11,300 ovarian cancer patients and followed them for diagnoses of SPCs until the end of 2015. Relative risks (RRs) of SPC in patients who had parents or siblings diagnosed with the same cancer (positive family history) were compared to those in patients without a family history (negative family history). Causes of death were compared between patients with and without SPC. Results: A total of 1,111 (9.8%) ovarian cancer patients developed SPC with a median follow-up of 8 years. The impact of a family history of cancer on the risk of the same cancer as SPC was significant for colon (RRpositive family history [95% CI] vs RRnegative family history [95% CI]: 4.95 [3.03–8.09] vs 2.00 [1.63–2.47]), lung (3.32 [1.88–5.84] vs 1.45 [1.16–1.83]), and breast (2.08 [1.58–2.73] vs 1.01 [0.88–1.15]) cancers. With a family history of any cancer, the RR for non-ovarian SPCs was 1.66 (1.54–1.74), in contrast to 1.38 (1.24–1.54) for SPCs without any family history (P-trend

Phylogenetic reconstruction of cancer cell populations remains challenging. There is a particular lack of tools that deconvolve clones based on copy number aberration analyses of multiple tumor biopsies separated in time and space from the same patient. This has hampered investigations of tumors rich in aneuploidy but few point mutations, as in many childhood cancers. Here, we present DEVOLUTION, an algorithm for subclonal deconvolution followed by phylogenetic reconstruction from bulk genotyping data. It integrates copy number and sequencing information across multiple tumor regions throughout the inference process, provided that the mutated clone fraction for each mutation is known. We validate DEVOLUTION on SNP-array data from 56 pediatric tumors comprising 253 tumor biopsies confirming concordance to biological mechanisms and show a robust performance on extensive simulations of bulk genotyping data.

Clonal deconvolution of mutational landscapes is crucial to understand the evolutionary dynamics of cancer. Two limiting factors for clonal deconvolution that have remained unresolved are variation in tumor cell fraction (TCF) and chromosomal copy number across different samples of the same tumor. We developed a semi-supervised algorithm that tracks variant calls through multi-sample spatiotemporal tumor data. While normalizing allele frequencies based on TCF it also adjusts for copy number changes at clonal deconvolution. Absent à priori copy number data, it rendersin silicocopy number estimations from bulk sequences. Using published and simulated tumor sequences, we reliably segregated clonal/subclonal variants even at low sequencing depth (∼50x). Given at least one pure tumor sample (>70% TCF), we could normalize and deconvolve paired samples down to a TCF of 40%. This renders a reliable clonal reconstruction well adapted to multi-regionally sampled solid tumor, which are often aneuploid and contaminated by non-cancer cells.

Familial clustering, twin concordance, and identification of high- and low-penetrance cancer predisposition variants support the idea that there are families that are at a high to moderate excess risk of cancer. To what extent there may be families that are protected from cancer is unknown. We wanted to test genetically whether cancer-free families share fewer breast, colorectal, and prostate cancer risk alleles than the population at large. We addressed this question by whole-genome sequencing (WGS) of 51 elderly cancer-free individuals whose numerous (ca. 1000) family members were found to be cancer-free (&lsquo, cancer-free families&rsquo, CFFs) based on face-to-face interviews. The average coverage of the 51 samples in the WGS was 42x. We compared cancer risk allele frequencies in cancer-free individuals with those in the general population available in public databases. The CFF members had fewer loss-of-function variants in suggested cancer predisposition genes compared to the ExAC data, and for high-risk cancer predisposition genes, no pathogenic variants were found in CFFs. For common low-penetrance breast, colorectal, and prostate cancer risk alleles, the results were not conclusive. The results suggest that, in line with twin and family studies, random environmental causes are so dominant that a clear demarcation of cancer-free populations using genetic data may not be feasible.

Second primary cancers (SPCs) are becoming a common cancer entity, which may interfere with survival in relatively benign first primary cancers. We examined the hypothesis that immune dysfunction may contribute to SPCs by assessing SPCs associated with known immune responsive skin cancers, invasive and in situ squamous cell carcinoma, Kaposi sarcoma, and Merkel cell carcinoma. Cancers were identified from the Swedish Cancer Registry from the year 1958 to 2015. Standardized relative risks were calculated bidirectionally for any SPC after skin cancer and for skin cancer as SPC. Over 80,000 first primary cancers were identified for each invasive and in situ squamous cell carcinoma of the skin. Bidirectional increased risks were observed for 26 cancers associated with invasive skin cancer; the Spearman rank correlation was 0.72 (P = 4.6 x 10(-5)). The highest bidirectional relative risks were for invasive and in situ skin cancer as SPCs (14.59 and 16.71, respectively). Remarkably high risks for second in situ squamous cell carcinoma of the skin were found after Kaposi sarcoma (685.68) and Merkel cell carcinoma (117.23). The high systematic bidirectional risks between immune responsive skin cancers and most other cancers suggest that immune suppression is a key mechanism contributing to an increased risk of SPCs.

Survival rates are increasing in patients with prostate cancer, and second primary cancers (SPCs) are becoming more common in these patients. However, the etiology and clinical consequences of SPCs are not well-known. We define the impact of family history on SPC and causes of mortality in these patients. A nation-wide cohort study based on the Swedish Family-Cancer Database covering 4.4 million men and 80,449 prostate cancers diagnosed between 1990 and 2015. Relative risks (RRs) and cumulative incidence for SPCs and for familial SPC were calculated for prostate cancer patients. SPC was diagnosed in 6,396 men and more than a third of these patients had a first-degree family history of any cancer; the familial risk was 1.37 (95% CI: 1.27–1.40), compared to 1.10 (1.08–1.16), without a family history. Cumulative incidence by the age of 83 years reached 21% for prostate cancer alone, 28% in those with SPC, and 35% in patients with SPC and family history. Family history was associated with the risk of seven specific SPCs, including colorectal, lung, kidney, bladder and skin (both melanoma and squamous cell) cancers, and leukemia. Colorectal and lung cancers were common SPCs, and family history doubled the risk of these SPCs. In patients with SPC, half of all causes of death were due to SPC and only 12.77% were due to prostate cancer. Most deaths in SPC were caused by lung and colorectal cancers. SPCs were an important cause of death in patients with prostate cancer and family history was an important risk factor for SPCs. Prevention of SPC should be essential when prostate cancer survival rates are being improved and this could start by conducting a thorough assessment of family history at the time of prostate cancer diagnosis.

Summary Background Patients with squamous cell skin cancer (SCC) have an excellent prognosis but second primary cancers (SPCs) weaken survival prospects. Family history is a known risk factor for cancer but whether it is a risk factor for SPC in patients with SCC is not known. Objectives To quantify the risk of family history on SPCs in patients with SCC and estimate survival probabilities of patients with SPCs depending on family history. Methods With 13 945 histologically verified SCCs, relative risks (RRs) were estimated for family history using a generalized regression model. For survival analysis, hazard ratios (HRs) were assessed using a multivariable Cox proportional-hazards model. Results Family history of invasive SCC increased risk of second invasive SCC [RR = 42·92, 95% confidence interval (CI) 33·69?50·32] compared with risk without family history (RR 19·12, 95% CI 17·88?21·08). Family history of any nonskin cancer in invasive SCC increased risk of the same cancers to be diagnosed as SPC (RRFH = 1·48, 95% CI 1·35?1·61 vs. RRno FH = 1·40, 95% CI 1·32?1·48); significant increases were observed for seven different nonskin cancers. Most results were replicated for in situ SCC. SPC was deleterious for survival irrespective of family history; HR for patients with SPC was 4·28 (95% CI 3·83?4·72) vs. those without SPC (1·04). Conclusions Family history of nonskin cancer was associated with approximately a doubling of risk for SPCs in patients with SCC. SPC increases the death rate in patients with SCC 3?4 times, irrespective of family history. Taking family history into account at SCC diagnosis may help prevention or early detection of SPCs. What's already known about this topic? Second primary cancers (SPCs) are frequently diagnosed in patients with invasive and in situ squamous cell carcinoma (SCC); some epidemiological studies suggest a link to immune dysfunction. Family history of cancer is a risk factor for practically all first primary cancers but whether it also influences risk of SPCs in patients with SCC is not known. The possible influence of family history on survival in patients with SCC remains to be established.

TO THE EDITOR: Myeloid malignancies are clonal proliferative diseases with shared but diverse phenotype characteristics; this classification includes (1) the myeloproliferative neoplasms (MPNs), polycythemia vera (PV), essential thrombocythemia (ET), and myelofibrosis (MF); (2) chronic myeloid

Uveal melanoma is a life-threatening disease for which data on germline predisposition are essentially limited to mutations in the BAP1 gene. Many risk factors are shared between uveal melanoma and cutaneous melanoma, and these include fair skin color and light eye color. We carried out a genome-wide association study on 590 uveal melanoma patients and 5199 controls. Using a P-value limit of 10 we identified 11 loci with related odds ratios for the risk alleles ranging from 1.32 to 1.78. The smallest P-value in the overall analysis reached 1.07 × 10 for rs3759710 at 14q32.11, which is intronic to TDP1 (tyrosyl-DNA phosphodiesterase 1). This locus emerged as a genome-wide significant association for uveal melanoma clinical subtypes with any chromosomal aberrations (P = 10) and presence of epithelioid cells (P = 10). TDP1 is a DNA repair enzyme capable of repairing many types of DNA damage, including oxidative DNA lesions which may be relevant for uveal melanoma. We additionally wanted to replicate the previous candidate locus for uveal melanoma at chromosome 5p15.33 intronic to the CLPTM1L gene. Our analysis gave an odds ratio of 1.23 (95% confidence interval: 1.09-1.38; P = 0.0008) for the C allele of rs421284 and 1.21 (95% confidence interval: 1.07-1.36; P = 0.002) for the C allele of rs452932. Our data thus replicated the association of uveal melanoma with the CLPTM1L locus. Our data on TDP1 offer an attractive model positing that oxidative damage in pigmented tissue may be an initiation event in uveal melanoma and the level of damage may be regulated by the degree and type of iris pigmentation.

While treatment for testicular cancer (TC) has become standardized after the 1980s with an associated significant improvement in patient survival, this has been accompanied by an increased risk of second primary cancers (SPCs). Patients were identified from the Swedish Cancer Registry spanning the years from 1980 to 2015, including 8788 individuals with primary TC and their SPCs. Relative risks (RRs) for SPC were calculated using the generalized Poisson regression model. SPCs were diagnosed in 9.4% of patients with TC and half of them were late onset cancers not common in the population in their 40s. Overall RR of SPCs (excluding second TC) was 1.30 (95%CI: 1.20-1.40), including high risks for seven solid cancers, non-Hodgkin lymphoma and leukemia. Second TC was the most common SPC and the RR of 17.19 (95%CI: 14.89-19.85) was the highest recorded. Cancers known to be fatal as first primary cancers were also fatal as SPC in TC patients. Survival at 30 years of follow-up was approximately 80% for TC patients without SPC but it decreased to 40% for patients with SPC. The unexpected finding that half of the identified SPCs were typical late onset cancers in the middle-aged population raises concerns that therapy may facilitate premature aging. The risks of SPC are clinically important for the long-term management of TC patients and the high-mortality calls for a future management strategy.

Eight novel loci implicate shared genetic etiology in multiple myeloma, AL amyloidosis, and monoclonal gammopathy of unknown significance

Genome-wide association study of monoclonal gammopathy of unknown significance (MGUS) : comparison with multiple myeloma

Improvement of survival in lymphocytic leukaemia has been accompanied by the occurrence of second primary cancer (SPCs). Based on Swedish Family Cancer Database, we applied bi-directional analyses in which relative risks (RRs) were calculated for any SPCs in patients with chronic lymphocytic leukaemia (CLL), acute lymphoblastic leukaemia (ALL) and hairy cell leukaemia (HCL) and the risks of these leukaemias as SPCs. After CLL, RRs were significant for 20 SPCs, and high for skin squamous cell cancer (2458 for insitu and 763 for invasive), Merkel cell carcinoma (1436), Hodgkin lymphoma (716) and Kaposi sarcoma (676). Conversely, 15 CLL cancer pairs were reciprocally increased. The increased risks were reciprocal for ALL and four cancers. RR for ALL was 1535 after myeloid neoplasia. HCL showed reciprocally increased RRs with non-Hodgkin lymphoma and melanoma. The concordance between RRs for bi-directional associations between CLL and different cancers, and HCL and different cancers was highly significant. For CLL (also for HCL), the bi-directional risks with skin cancers and other immune-related cancers suggest the probable involvement of immune dysfunction. For ALL, treatment may contribute to risks of multiple SPCs. Increased risk of ALL after haematological neoplasms may indicate bone marrow dysfunction. These findings may help guide treatment decisions and prognostic assessment.

BackgroundMalignant melanoma (MM) patients are at increasing risk of developing second primary cancers (SPCs). We assessed mortality and risk of SPCs in MM patients with siblings or parents affected with same cancer compared with that of the general population.MethodsWe used the Swedish Family-Cancer Database to assess relative risks (RRs) and causes of death in SPCs until 2015 in patients with a MM diagnosis between 1958 and 2015. We identified 35 451patients with MM among whom 3212 received a subsequent diagnosis of SPC. RRs of SPCs after MM diagnosis were calculated stratifying over concordant family history of cancer in first-degree relatives.ResultsFamilial RRs were increased for second melanoma (RR = 19.28, 95% CI = 16.71 to 22.25), squamous cell skin cancer (RR = 7.58, 95% CI = 5.57 to 10.29), leukemia (RR = 5.69, 95% CI = 2.96 to 10.94), bladder (RR = 4.15, 95% CI = 2.50 to 6.89), ovarian (RR = 3.89, 95% CI = 1.46 to 10.37), kidney cancer (RR = 3.77, 95% CI = 1.57 to 9.06), cancer of unknown primary (RR = 3.67, 95% CI = 1.65 to 8.16), nervous system (RR = 2.88, 95% CI = 1.20 to 6.93), breast (RR = 2.34, 95% CI = 1.92 to 2.84), lung (RR = 2.24, 95% CI = 1.50 to 3.35), and prostate cancer (RR = 2.22, 95% CI = 1.89 to 2.61) with statistical significance. For all cancers, familial RR was in excess (2.09, 95% CI = 2.02 to 2.16 vs 1.78, 95% CI = 1.69 to 1.87; Ptrend ConclusionsSPCs appear higher with prior family history of cancer and contribute to mortality. SPC was the most common cause of death in patients with SPC and is almost uniformly the major contributing cause of death for all cancer sites. For improved survival in MM patients, prevention and early detection of SPCs would be important.

Background Recent identification of 10 germline variants predisposing to monoclonal gammopathy of undetermined significance (MGUS) explicates genetic dependency of this asymptomatic precursor condition with multiple myeloma (MM). Yet much of genetic burden as well as functional links remain unexplained. We propose a workflow to expand the search for susceptibility loci with genome-wide interaction and for subsequent identification of genetic clusters and pathways. Methods Polygenic interaction analysis on 243 cases/1285 controls identified 14 paired risk loci belonging to unique chromosomal bands which were then replicated in two independent sets (case only study, 82 individuals; case/control study 236 cases/ 2484 controls). Further investigation on gene-set enrichment, regulatory pathway and genetic network was carried out with stand-alone in silico tools separately for both interaction and genome-wide association study-detected risk loci. Results Intronic-PREX1 (20q13.13), a reported locus predisposing to MM was confirmed to have contribution to excess MGUS risk in interaction with SETBP1, a well-established candidate predisposing to myeloid malignancies. Pathway enrichment showed B cell receptor signaling pathway (P

PASCAL gene set enrichment analysis results at 1% level of significance. (DOCX 20 kb)

All detected pathways mutually discovered in both MAGENTA and PASCAL at a 5% level of combined significance. (DOCX 21 kb)

MAGENTA gene set enrichment analysis results at 1% level of significance. (DOCX 20 kb)

Number of overlaps in number of SNPs prior quality control between different chips used in genotyping. Chip numbers are defined in Additional file 10. (DOCX 19 kb)

Overlapped interactions from INTERSNP and CASSI W-Z interaction tests on discovery set. Description: SNP1 and SNP2 are the two SNP candidates of a pair from the discovery set population belonging to chromosomes denote by Chr1 and Chr2; gene1 and gene2 are the corresponding genes annotated to SNP1(s) and SNP2(s), respectively. W-Z P value is Wellek Ziegler case-control test p-value from CASSI and INTERSNP P value is full log-linear test p-value from INTERSNP; BP is base pair. IN: INTERSNP; CAS: CASSI. (DOCX 22 kb)

Top interactions from W-Z interaction test on the replication set. Description: SNP1 and SNP2 are the two SNP candidates of a pair from the replication set population belonging to chromosomes denote by Chr1 and Chr2; gene1 and gene2 are the corresponding genes annotated to SNP1 and SNP2, respectively. W-Z P value is Wellek Ziegler case-control test p-value; BP is base pair. (DOCX 22 kb)

Gene set enrichment analysis in genetic network with STRING. Description: Based on the indexing nodes and the additional predicted first order interacting m=nodes, STRING performs enrichment analysis on several molecular, biological, cellular process related pathway analysis with Gene Onltology (GO) and KEGG database. All tests are performed with guilt by association assumption and P values are corrected for multiple testing. A protein-protein enrichment index is reported with analysis depicting level of confidence in the detected enriched processes which is reported to be 0.0039 (significant at 5% level). (DOCX 21 kb)

Top interactions from W-Z case-only test in confirmation set. Description: SNP1 and SNP2 are the two corresponding SNP candidates of a pair from the case-only population belonging to chromosomes denote by Chr1 and Chr2; gene1 and gene2 are the corresponding genes annotated to SNP1 and SNP2, respectively. W-Z P value is Wellek Ziegler case-only test p-value; BP is base pair. (DOCX 21 kb)

Introduction With improving survival in ovarian cancer, second primary cancers (SPCs) and their etiological underpinnings are becoming an issue. How family history may influence the occurrence of SPCs and the related mortality is not well known. We defined familial cancer through identity of cancer in the first-degree relatives (parents or siblings) and patient’s SPC, and explored the impact of family history on the risk of SPCs and related mortality. Material and methods Based on the Swedish Family-Cancer Database, we identified ovarian cancer patients among the 0–83 year old second generation and followed them for diagnoses of SPCs to the end of 2015. Relative risks (RRs) of SPC estimated from Poisson regression in ovarian cancer patients who had first-degree relatives (positive family history) affected by the same cancer were compared to the patients who didn’t have (negative family history) with trend test. Causes of death were compared between patients with and without SPC. Results and discussions A total of 11 300 ovarian cancers were diagnosed among 0–83 year old women of whom 1111 (9.8%) later developed SPC. Accounting for 67.6% of all patients with a SPC diagnosis, 751 had at least one first-degree relative diagnosed with cancer, for 129 of whom it was the same second cancer as in the family member. The trend test for family history of concordant SPC was significant for colon (RR positive family history vs. RR negative family history5.00 vs. 2.01), lung (3.44 vs. 1.46), breast (2.11 vs. 1.03) and endometrial (6.56 vs. 2.39) cancers. With any family history (concordant or discordant), RR for SPCs was 1.97 in contrast to 1.52 for SPCs without any family history (p-trend Conclusion In summary, close to 10% of ovarian cancer patients were diagnosed with SPC, 2/3 of whom had a first-degree relative diagnosed with cancer. Family history contributed to increasing numbers of SPCs and high familial associations were found for cancers that are known to manifest in ovarian cancer-related cancer syndromes. We conclude, considering family history at diagnosis of ovarian cancer may alert physicians about a syndromatic background, management of which may help the patient as well her family members.

Introduction Multiple myeloma (MM) is a plasma cell dyscrasia characterised by proliferation of monoclonal plasma cells. As one of the most prevalent haematological malignancies, MM is genetically heterogeneous. Although 17 individual MM susceptibility loci have been identified, their inherent biological mechanism is sparsely understood. We carried out a polygenic interaction analysis with published whole-genome association studies (GWASs) to further characterise MM susceptibility with inflated genomic resolution in order to locate seemingly aberrant variations having temporal aggregation of risk. Material and methods Single nucleotide polymorphisms data from two MM GWAS representing 3999 cases and 7266 controls were subjected to genome-wide interaction analysis and followed-up with a meta-analysis. The identified loci were used for consequent gene set enrichment and tissue expression prioritisation to obtain functional evidence. Causal dependency between sentinel loci and functional variants was then interrogated with expression quantitative trait loci subject to summary data-based Mendelian randomization. Patient samples and relevant clinico-pathological information was obtained conditional on written informed consent and was subject to approval of corresponding ethical review boards at respective study centres in accordance with the tenets of Declaration of Helsinki Results and discussions A total of sixteen novel interacting pairs were identified along with indication of differential regulation in two principal signalling cascade families. Several previously identified and novel chromosomal regions influencing hematopoietic malignancies and contributing to pluripotent B-cell differentiation, survival, proliferation and apoptosis were identified. These loci were suggested to influence immune response and regulate immunoglobulin class-switch. Tissue/cell-type enrichment analysis showed that the genes associated with the identified loci were highly expressed in hemic-immune system tissue types and immune-related cell types. Conclusion Our polygenic interaction analysis renders novel insight into genetic susceptibility in MM. Related pathways provide some basic understanding of functional relation between discovered candidates as well as a biological basis of predisposition.