Identifying new candidate colorectal cancer (CRC) genes and mutations are important for clinical cancer prevention as well as in cancer care. Genetic counseling is already implemented for known ...high‐risk variants; however, the majority of CRC are of unknown causes. In our study, 110 CRC patients in 55 Swedish families with a strong history of CRC but unknown genetic causes were analyzed with the aim of identifying novel candidate CRC predisposing genes. Exome sequencing was used to identify rare and high‐impact variants enriched in the families. No clear pathogenic variants were found in known CRC predisposing genes; however, potential pathogenic variants in novel CRC predisposing genes were identified. Over 3000 variants with minor allele frequency (MAF) <0.01 and Combined Annotation Dependent Depletion (CADD) > 20 were seen aggregating in the CRC families. Of those, 27 variants with MAF < 0.001 and CADD>25 were considered high‐risk mutations. Interestingly, more than half of the high‐risk variants were detected in three families, suggesting cumulating contribution of several variants to CRC. In summary, our study shows that despite a strong history of CRC within families, identifying pathogenic variants is challenging. In a small number of families, few rare mutations were shared by affected family members. This could indicate that in the absence of known CRC predisposing genes, a cumulating contribution of mutations leads to CRC observed in these families.
What's new?
Genetic counseling is already implemented in colorectal cancer for known high‐risk variants. However, the majority of cases are of unknown causes. In this study, 110 patients in 55 Swedish families with a strong history of colorectal cancer but unknown genetic causes were analyzed to identify novel candidate predisposing genes. Exome‐sequencing revealed several potential pathogenic variants in novel colorectal cancer predisposing genes, while variants in known predisposing genes were not seen. Many of the variants were observed within the same families, which potentially indicates a cumulative contribution of mutations and emphasises the complexity of colorectal cancer.
The amount of data available from genomic medicine has revolutionized the approach to identify the determinants underlying many rare diseases. The task of confirming a genotype–phenotype causality ...for a patient affected with a rare genetic disease is often challenging. In this context, the establishment of the Matchmaker Exchange (MME) network has assumed a pivotal role in bridging heterogeneous patient information stored on different medical and research servers. MME has made it possible to solve rare disease cases by “matching” the genotypic and phenotypic characteristics of a patient of interest with patient data available at other clinical facilities participating in the network. Here, we present PatientMatcher (https://github.com/Clinical-Genomics/patientMatcher), an open‐source Python and MongoDB‐based software solution developed by Clinical Genomics facility at the Science for Life Laboratory in Stockholm. PatientMatcher is designed as a standalone MME server, but can easily communicate via REST API with external applications managing genetic analyses and patient data. The MME node is being implemented in clinical routine in collaboration with the Genomic Medicine Center Karolinska at the Karolinska University Hospital. PatientMatcher is written to implement the MME API and provides several customizable settings, including a custom‐fit similarity score algorithm and adjustable matching results notifications.
Approximately 5% of patients with colorectal cancer (CRC) have a Mendelian predisposition for the disease. Identification of the disease‐causing genetic variant enables carrier testing and tailored ...cancer prevention within affected families. To determine the panorama and genetic variation of Mendelian CRC syndromes among referrals at the cancer genetics clinics in Sweden, 850 patients clinically selected for CRC genetic investigation were included in a prospective study that tested for all major hereditary polyposis and nonpolyposis CRC conditions. Genetically defined syndromes were diagnosed in 11% of the patients. Lynch syndrome was predominant (n = 73) followed by familial adenomatous polyposis (n = 12) and MUTYH‐associated polyposis (n = 8); the latter of which two patients presented with CRC before polyposis was evident. One patient with a history of adolescent‐onset CRC and polyposis had biallelic disease‐causing variants diagnostic for constitutional mismatch repair deficiency syndrome. Post‐study review of detected variants of unknown clinical significance (n = 129) resulted in the reclassification of variants as likely benign (n = 59) or as diagnostic for Lynch syndrome (n = 2). Our results reveal the panorama of Mendelian CRC syndromes at the cancer genetics clinics in Sweden and show that unified testing for polyposis and nonpolyposis CRC conditions as well as regular reexamination of sequence data improve the diagnostic yield.
Colorectal cancer (CRC), prostate cancer (PrC), and gastric cancer (GC) are common worldwide, and the incidence is to a certain extent dependent on genetics. We have recently shown that in families ...with more than one case of CRC, the risk of other malignancies is increased. We therefore suggested the presence of not yet described CRC syndromes. In this study, we have searched for genetic susceptibility loci for potential cancer syndromes involving CRC combined with PrC and/or GC. We have performed SNP (single‐nucleotide polymorphism)‐based linkage analyses in 45 families with CRC, PrC, and GC. In the regions with suggested linkage, we performed exome and association haplotype analyses. Five loci generated a high logarithm of odds (HLOD) score >2, suggestive of linkage, in chromosome bands 1q31‐32, 1q24‐25, 6q25‐26, 18p11‐q11, and Xp11. Exome analysis detected no potential pathogenic sequence variants. The haplotype association study showed that one of the top five haplotypes with the lowest P value in the chromosome band 6q25 interestingly was found in the family which contributed the most to the increased HLOD at that locus. This study supports a suggested hereditary cancer syndrome involving CRC and PrC and indicates a location at 6q25. The impact of this locus needs to be confirmed in additional studies.
Background Preventive programs for individuals who have high lifetime risks of colorectal cancer may reduce disease morbidity and mortality. Thus, it is important to identify the factors that are ...associated with hereditary colorectal cancer and to monitor the effects of tailored surveillance. In particular, patients with Lynch syndrome, hereditary nonpolyposis colorectal cancer (HNPCC), have an increased risk to develop colorectal cancer at an early age. The syndrome is explained by germline mutations in DNA mismatch repair (MMR) genes, and there is a need for diagnostic tools to preselect patients for genetic testing to diagnose those with HNPCC. Methods Patients (n = 112) from 285 families who were counseled between 1990 and 2005 at a clinic for patients at high risk for HNPCC were selected for screening to detect mutations in MMR genes MLH1, MSH2, MSH6, and PMS2 based on family history, microsatellite instability (MSI), and immunohistochemical analysis of MMR protein expression. Tumors were also screened for BRAF V600E mutations; patients with the mutation were considered as non-HNPCC. Results Among the 112 patients who were selected for screening, 69 had germline MMR mutations (58 pathogenic and 11 of unknown biologic relevance). Sixteen of the 69 mutations (23%) were missense mutations. Among patients with MSI-positive tumors, pathogenic MMR mutations were found in 38 of 43 (88%) of patients in families who met Amsterdam criteria and in 13 of 22 (59%) of patients in families who did not. Among patients with MSI-negative tumors, pathogenic MMR mutations were found in 5 of 17 (29%) of families meeting Amsterdam criteria and in 1 of 30 (3%) of non-Amsterdam families with one patient younger than age 50 years. In three patients with MSI-negative tumors who had pathogenic mutations in MLH1 or MSH6, immunohistochemistry showed loss of the mutated protein. Conclusion Our findings suggest that missense MMR gene mutations are common in HNPCC and that germline MMR mutations are also found in patients with MSI-negative tumors.
We have investigated 20 consanguineous families with multiple children affected by rare disorders. Detailed clinical examinations, exome sequencing of affected as well as unaffected family members ...and further validation of likely pathogenic variants were performed. In 16/20 families, we identified pathogenic variants in autosomal recessive disease genes (ALMS1, PIGT, FLVCR2, TFG, CYP7B1, ALG14, EXOSC3, MEGF10, ASAH1, WDR62, ASPM, PNPO, ERCC5, KIAA1109, RIPK4, MAN1B1). A number of these genes have only rarely been reported previously and our findings thus confirm them as disease genes, further delineate the associated phenotypes and expand the mutation spectrum with reports of novel variants. We highlight the findings in two affected siblings with splice altering variants in ALG14 and propose a new clinical entity, which includes severe intellectual disability, epilepsy, behavioral problems and mild dysmorphic features, caused by biallelic variants in ALG14.
Abstract Background Spinocerebellar ataxia 4 (SCA4), characterized in 1996, features adult‐onset ataxia, polyneuropathy, and linkage to chromosome 16q22.1; its underlying mutation has remained ...elusive. Objective To explore the radiological and neuropathological abnormalities in the entire neuroaxis in SCA4 and search for its mutation. Methods Three Swedish families with undiagnosed ataxia went through clinical, neurophysiological, and neuroimaging tests, including PET studies and genetic investigations. In four cases, neuropathological assessments of the neuroaxis were performed. Genetic testing included short read whole genome sequencing, short tandem repeat analysis with ExpansionHunter de novo, and long read sequencing. Results Novel features for SCA4 include dysautonomia, motor neuron affection, and abnormal eye movements. We found evidence of anticipation; neuroimaging demonstrated atrophy in the cerebellum, brainstem, and spinal cord. 18 FFDG‐PET demonstrated brain hypometabolism and 11 CFlumazenil‐PET reduced binding in several brain lobes, insula, thalamus, hypothalamus, and cerebellum. Moderate to severe loss of Purkinje cells in the cerebellum and of motor neurons in the anterior horns of the spinal cord along with pronounced degeneration of posterior tracts was also found. Intranuclear, mainly neuronal, inclusions positive for p62 and ubiquitin were sparse but widespread in the CNS. This finding prompted assessment for nucleotide expansions. A polyglycine stretch encoding GGC expansions in the last exon of the zink finger homeobox 3 gene was identified segregating with disease and not found in 1000 controls. Conclusions SCA4 is a neurodegenerative disease caused by a novel GGC expansion in the coding region of ZFHX3 , and its spectrum is expanded to include dysautonomia and neuromuscular manifestations.
Aim
To elucidate the natural course of benign paroxysmal torticollis, the relationship of this disorder to migraine and other paroxysmal diseases, and to analyse candidate genes.
Method
This was a ...case series of children with benign paroxysmal torticollis of infancy (BPTI) diagnosed from 1998 to 2005, at Astrid Lindgren Children's Hospital, Stockholm, Sweden. A neurological examination and a formalized motor assessment were performed from 2005 to 2007. At a second follow‐up, in 2014 to 2015, the children and their parents were interviewed and candidate genes analysed.
Results
The mean age of the eight females and three males included in the second follow‐up was 13 years 9 months (SD 2y 2mo). All motor assessments were normal. Five had developed migraine, abdominal migraine, and/or cyclic vomiting. Prophylactic treatment or migraine‐specific medication during attacks were not needed. No paroxysmal tonic upgaze, benign paroxysmal vertigo, epilepsy, episodic ataxia, or paroxysmal dyskinesia was reported. Rare genetic variants in CACNA1A and ATP1A2 were found in two children. Five had a family history of migraine.
Interpretation
BPTI is transient and does not lead to neurological sequelae. Most children afflicted experience either a mild migraine or no paroxysmal disorder at all in their adolescence. Genetic variants in candidate genes were few, indicating potential genetic heterogeneity.
What this paper adds
After resolution of their benign paroxysmal torticollis of infancy (BPTI), children display no gross motor delay.
Most adolescents who previously had BPTI have not developed migraine.
No mutations in candidate genes, known to cause hemiplegic migraine, were found.
Associated symptoms are often lacking during episodes of torticollis.
Resumen
La torticolis paroxística de la infancia no deja secuelas neurológicas
Objetivo
Dilucidar el curso natural de la tortícolis paroxística benigna, su relación con la migraña y otras enfermedades paroxísticas; y, analizar genes candidatos.
Método
Esta es una serie de casos con tortícolis paroxística benigna de la infancia (BPTI) diagnosticados entre 1998 y el 2005, en el Hospital de niños Astrid Lindgren de Estocolmo Suecia. Fue realizado un examen neurológico y una evaluación motriz formal desde el año 2005 al 2007. Un segundo seguimiento fue realizado entre el 2014 y el 2015. Los niños y sus padres fueron entrevistados y se analizaron genes candidatos.
Resultados
La edad promedio de 8 niñas y 3 niños incluidos en el segundo seguimiento fue de 13 años 9 meses. Todas las evaluaciones fueron normales. Cinco desarrollaron migraña, migraña abdominal y/o vómitos cíclicos. Los niños no requirieron tratamiento específico para la migraña durante los ataques ni profilaxis. No fue reportado elevación tónica de la mirada, vértigo paroxístico benigno, epilepsia, ataxia episódica o disquinesia paroxística. En dos niños fueron encontrados variantes genéticas inusuales en los genes CACNA1A y ATP1A2. Cinco tenían historia familiar de migraña.
Interpretación
BPTI es un fenómeno transitorio y los niños afectados son neurológicamente sanos y sólo desarrollan una migraña leve en la adolescencia. Las variaciones genéticas en los genes candidatos fueron escasas, indicando una probable heterogenecidad genética.
Resumo
Torcicolo paroxístico benigno da infância não causa sequelas neurológicas
Objetivo
Elucidar o curso natural do torcicolo paroxístico benigno, a relação desta desordem com enxaqueca e outas desordens paroxísticas, e analisar genes candidatos.
Método
Esta foi uma série de casos de crianças com torcicolo paroxístico benigno da infância (TPBI) diagnosticados de 1998 a 2005, no Hospital Pediátrico Astrid Lindgren, Estocolmo, Suécia. Um exame neurológico e uma avaliação motora fomal foram realizados de 2005 a 2007. Em um segundo acompanhamento, em 2014‐2015, as crianças e seus pais foram entrevistados, e genes candidatos foram analisados.
Resultados
A média de idade das oito participantes do sexo feminino e três do masculino incluídos no segundo acompanhamento foi 13 anos e 9 meses (DP 2a2m). Todas as avaliações motoras foram normais. Cinco desenvolveram enxaqueca, enxaqueca abdominal, e/ou vômito cíclico. O tratamento profilático ou medicação específica para enxaqueca durante os ataques não foram necessários. Nenhum desvio do olhar tônico paroxístico, vertigem paroxística benigna, epilepsia, ataxia episódica, ou discinesia paroxística foi relatado. Variantes genéticas raras nos genes CACNA1A e ATP1A2 foram encontradas em duas crianças. Cinco tinham histórico familiar de enxaqueca.
Interpretação
O TPBI é transiente e a maior parte das crianças atingidas são neurologicamente saudáveis ou apresentam apenas enxaqueca leve na adolescência. Variantes genéticas nos genes candidatos foram pouco frequentes, indicando heterogeneidade genética potencial.
What this paper adds
After resolution of their benign paroxysmal torticollis of infancy (BPTI), children display no gross motor delay.
Most adolescents who previously had BPTI have not developed migraine.
No mutations in candidate genes, known to cause hemiplegic migraine, were found.
Associated symptoms are often lacking during episodes of torticollis.
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This article is commented on by Blumkin on pages 1196–1197 of this issue.
Skeletal ciliopathies are a heterogenous group of disorders with overlapping clinical and radiographic features including bone dysplasia and internal abnormalities. To date, pathogenic variants in at ...least 30 genes, coding for different structural cilia proteins, are reported to cause skeletal ciliopathies. Here, we summarize genetic and phenotypic features of 34 affected individuals from 29 families with skeletal ciliopathies. Molecular diagnostic testing was performed using massively parallel sequencing (MPS) in combination with copy number variant (CNV) analyses and in silico filtering for variants in known skeletal ciliopathy genes. We identified biallelic disease-causing variants in seven genes: DYNC2H1, KIAA0753, WDR19, C2CD3, TTC21B, EVC, and EVC2. Four variants located in non-canonical splice sites of DYNC2H1, EVC, and KIAA0753 led to aberrant splicing that was shown by sequencing of cDNA. Furthermore, CNV analyses showed an intragenic deletion of DYNC2H1 in one individual and a 6.7 Mb de novo deletion on chromosome 1q24q25 in another. In five unsolved cases, MPS was performed in family setting. In one proband we identified a de novo variant in PRKACA and in another we found a homozygous intragenic deletion of IFT74, removing the first coding exon and leading to expression of a shorter message predicted to result in loss of 40 amino acids at the N-terminus. These findings establish IFT74 as a new skeletal ciliopathy gene. In conclusion, combined single nucleotide variant, CNV and cDNA analyses lead to a high yield of genetic diagnoses (90%) in a cohort of patients with skeletal ciliopathies.
Background
De novo variants are a common cause to rare intellectual disability syndromes, associated with low recurrence risk. However, when such variants occur pre‐zygotically in parental germ ...cells, the recurrence risk might be higher. Still, the recurrence risk estimates are mainly based on empirical data and the prevalence of germline mosaicism is often unknown.
Methods
To establish the prevalence of mosaicism in parents of children with intellectual disability syndromes caused by de novo variants, we performed droplet digital PCR on DNA extracted from blood (43 trios), and sperm (31 fathers).
Results
We detected low‐level mosaicism in sperm‐derived DNA but not in blood in the father of a child with Kleefstra syndrome caused by an EHMT1 variant. Additionally, we found a higher level of paternal mosaicism in sperm compared to blood in the father of a child with Gillespie syndrome caused by an ITPR1 variant.
Conclusion
By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
By employing droplet digital PCR, we detected paternal germline mosaicism in two intellectual disability syndromes. In both cases, the mosaicism level was higher in sperm than blood, indicating that analysis of blood alone may underestimate germline mosaicism. Therefore, sperm analysis can be clinically useful to establish the recurrence risk for parents and improve genetic counselling.
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