Copy Number Variation Analysis in Familial BRCA1/2-Negative Finnish Breast and Ovarian Cancer

Background Inherited factors predisposing individuals to breast and ovarian cancer are largely unidentified in a majority of families with hereditary breast and ovarian cancer (HBOC). We aimed to identify germline copy number variations (CNVs) contributing to HBOC susceptibility in the Finnish population. Methods A cohort of 84 HBOC individuals (negative for BRCA1/2-founder mutations and pre-screened for the most common breast cancer genes) and 36 healthy controls were analysed with a genome-wide SNP array. CNV-affecting genes were further studied by Gene Ontology term enrichment, pathway analyses, and database searches to reveal genes with potential for breast and ovarian cancer predisposition. CNVs that were considered to be important were validated and genotyped in 20 additional HBOC individuals (6 CNVs) and in additional healthy controls (5 CNVs) by qPCR. Results An intronic deletion in the EPHA3 receptor tyrosine kinase was enriched in HBOC individuals (12 of 101, 11.9%) compared with controls (27 of 432, 6.3%) (OR = 1.96; P = 0.055). EPHA3 was identified in several enriched molecular functions including receptor activity. Both a novel intronic deletion in the CSMD1 tumor suppressor gene and a homozygous intergenic deletion at 5q15 were identified in 1 of 101 (1.0%) HBOC individuals but were very rare (1 of 436, 0.2% and 1 of 899, 0.1%, respectively) in healthy controls suggesting that these variants confer disease susceptibility. Conclusion This study reveals new information regarding the germline CNVs that likely contribute to HBOC susceptibility in Finland. This information may be used to facilitate the genetic counselling of HBOC individuals but the preliminary results warrant additional studies of a larger study groupPublic Library of Science open acces

Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland

The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case.Peer reviewe

Exome sequencing reveals predominantly de novo variants in disorders with intellectual disability (ID) in the founder population of Finland

The genetics of autosomal recessive intellectual disability (ARID) has mainly been studied in consanguineous families, however, founder populations may also be of interest to study intellectual disability (ID) and the contribution of ARID. Here, we used a genotype-driven approach to study the genetic landscape of ID in the founder population of Finland. A total of 39 families with syndromic and non-syndromic ID were analyzed using exome sequencing, which revealed a variant in a known ID gene in 27 families. Notably, 75% of these variants in known ID genes were de novo or suspected de novo (64% autosomal dominant; 11% X-linked) and 25% were inherited (14% autosomal recessive; 7% X-linked; and 4% autosomal dominant). A dual molecular diagnosis was suggested in two families (5%). Via additional analysis and molecular testing, we identified three cases with an abnormal molecular karyotype, including chr21q22.12q22.2 uniparental disomy with a mosaic interstitial 2.7 Mb deletion covering DYRK1A and KCNJ6. Overall, a pathogenic or likely pathogenic variant was identified in 64% (25/39) of the families. Last, we report an alternate inheritance model for 3 known ID genes (UBA7, DDX47, DHX58) and discuss potential candidate genes for ID, including SYPL1 and ERGIC3 with homozygous founder variants and de novo variants in POLR2F and DNAH3. In summary, similar to other European populations, de novo variants were the most common variants underlying ID in the studied Finnish population, with limited contribution of ARID to ID etiology, though mainly driven by founder and potential founder variation in the latter case

ATM c.7570G>C is a high-risk allele for breast cancer

Abstract ATM is generally described as a moderate-risk breast cancer susceptibility gene. However, some of ATM variants might encounter higher risk. ATM c.7570G>C, p.Ala2524Pro, (rs769142993) is a pathogenic Finnish founder variant causative for recessively inherited ataxia-telangiectasia. At cellular level, it has been reported to have a dominant-negative effect. ATM c.7570G>C has recurrently been described in Finnish breast cancer families and unselected case cohorts collected from different parts of the country, but the rarity of the allele (MAF 0.0002772 in Finns) and lack of confirming segregation analyses have prevented any conclusive risk estimates. Here, we describe seven families from genetic counseling units with ATM c.7570G>C variant showing co-segregation with breast cancer. Further analysis of the unselected breast cancer cohort from Northern Finland (n = 1822), a geographical region previously indicated to have enrichment of the variant, demonstrated that c.7570G>C significantly associates with breast cancer, and the risk is estimated as high (odds ratio [OR] = 8.5, 95% confidence interval [CI] = 1.04-62.46, P = .018). Altogether, these results place ATM c.7570G>C variant among the high-risk alleles for breast cancer, which should be taken into consideration in genetic counseling

Germline EMSY sequence alterations in hereditary breast cancer and ovarian cancer families

Abstract Background BRCA1 and BRCA2 mutations explain approximately one-fifth of the inherited susceptibility in high-risk Finnish hereditary breast and ovarian cancer (HBOC) families. EMSY is located in the breast cancer-associated chromosomal region 11q13. The EMSY gene encodes a BRCA2-interacting protein that has been implicated in DNA damage repair and genomic instability. We analysed the role of germline EMSY variation in breast/ovarian cancer predisposition. The present study describes the first EMSY screening in patients with high familial risk for this disease. Methods Index individuals from 71 high-risk, BRCA1/2-negative HBOC families were screened for germline EMSY sequence alterations in protein coding regions and exon-intron boundaries using Sanger sequencing and TaqMan assays. The identified variants were further screened in 36 Finnish HBOC patients and 904 controls. Moreover, one novel intronic deletion was screened in a cohort of 404 breast cancer patients unselected for family history. Haplotype block structure and the association of haplotypes with breast/ovarian cancer were analysed using Haploview. The functionality of the identified variants was predicted using Haploreg, RegulomeDB, Human Splicing Finder, and Pathogenic-or-Not-Pipeline 2. Results Altogether, 12 germline EMSY variants were observed. Two alterations were located in the coding region, five alterations were intronic, and five alterations were located in the 3'untranslated region (UTR). Variant frequencies did not significantly differ between cases and controls. The novel variant, c.2709 + 122delT, was detected in 1 out of 107 (0.9%) breast cancer patients, and the carrier showed a bilateral form of the disease. The deletion was absent in 897 controls (OR = 25.28; P = 0.1) and in 404 breast cancer patients unselected for family history. No haplotype was identified to increase the risk of breast/ovarian cancer. Functional analyses suggested that variants, particularly in the 3'UTR, were located within regulatory elements. The novel deletion was predicted to affect splicing regulatory elements. Conclusions These results suggest that the identified EMSY variants are likely neutral at the population level. However, these variants may contribute to breast/ovarian cancer risk in single families. Additional analyses are warranted for rare novel intronic deletions and the 3'UTR variants predicted to have functional roles

Validated copy number variations.

<p>Abbreviations: CI = confidence interval; na = not available; OR = odds ratio.</p>a<p>According to the NCBI Genome Build 36.1 (hg 18). Exact start and end positions of the CNVs are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071802#pone.0071802.s002" target="_blank">Table S1</a>.</p>b<p>Size reported in HBOC individuals analysed in the SNP array (may vary between individuals).</p>c<p>Combined frequencies of original cohort of 81 HBOC individuals (analysed in the SNP array) and cohort of 20 additional HBOC individuals (genotyped by TaqMan® Copy Number Assays). CNVs in the 2q34, 5q15, 8p23.2, and 17q21.31 regions were not observed in additional cohort of 20 HBOC individuals. Heterozygous deletion (copy number 1) in the 3p11.1 region was also identified in 4 out of the 20 additional HBOC individuals (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071802#pone.0071802.s005" target="_blank">File S2</a>). Heterozygous duplication (copy number 3) in the 19q13.41 region was also identified in 3 out of the 20 additional HBOC individuals (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071802#pone.0071802.s005" target="_blank">File S2</a>). Homozygous duplication (copy number 4) in the 19q13.41 region was identified in 1 out of the 20 additional HBOC individuals (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071802#pone.0071802.s005" target="_blank">File S2</a>).</p>d<p>Thirty-five controls were first analyzed in the SNP array. CNVs were also screened in additional controls by TaqMan® Copy Number Assays (excluding <i>BRCA1</i> affecting CNV since large deletions in <i>BRCA1</i> coding regions are known to associate with breast and ovarian cancer susceptibility).</p>e<p>Search against the Database of Genomic Variants (DGV).</p>f<p>Deletion in the 5q15 region was homozygous (copy number 0) in 1 out of the 101 (0.010) HBOC individuals and in 1 out of the 899 (0.001) controls and heterozygous (copy number 1) in 4 out of the 101 (0.040) HBOC individuals and in 56 out of the 899 (0.062) controls.</p>g<p>Duplication in the 19q13.41 region was homozygous (copy number 4) in 4 out of the 101 (0.040) HBOC individuals and in 3 out of the 334 (0.009) controls and heterozygous (copy number 3) in 7 out of the 101 (0.069) HBOC individuals and in 31 out of the 334 (0.093) controls.</p

Family 128 pedigree.

<p>Index individual carries a novel 10.8 kb deletion in the 8p23.2. The deletion affects intronic region of the <i>CSMD1</i> tumor suppressor gene. Females are marked with circles and males are marked with squares. Number in circle or squares indicates descendants. Index individual is marked with an arrow. Breast cancers are marked with black circles with the age at diagnosis. Other cancers are marked with grey and specified with the age at diagnosis (Br: breast, GI: gastrointestinal, Mel: melanoma). Deceased individuals are marked with a slash. Current ages of healthy females are presented in the paternal side of the family. In addition, the current age of index’s healthy daughter is indicated. Generations are marked with the Roman numerals on the left.</p

The clinical characteristics and family cancer history for HBOC individuals analysed in the SNP array with the six validated copy number variations.

*<p>Homozygous CNV.</p><p>Abbreviations: BCC = Basal-cell carsinoma; Bil. Br = bilateral breast; Br = breast; Ca = cancer; Cer = cervix in situ carsinoma/cervix carsinoma; Co = colon; Dg = diagnosis; Del = deletion; Duct = ductal; Dup = duplication; Eso = esophagus; GI = gastrointestinal; gr = grade; Int = intestine; Kid = kidney; Lob = lobular; Mel = melanoma; na = not available; Ov = ovary; Panc = pancreatic; Sto = stomach; Thy = thyroid; To = tongue; Ute = ute. Cancers diagnosed in the paternal side of the family are presented in italics. Cancers diagnosed in siblings or their children of the index patients are underlined. Cancers diagnosed in the children of the index patients are presented in bold.</p

Family 249 pedigree.

<p>Index individual carries a novel 59.0 kb deletion in the 2q34 locus. The deletion affects intronic region of the <i>ERBB4</i> gene, which encodes a receptor tyrosine kinase family member that plays an important role in several cellular signalling pathways. The deletion was also identified in index’s mother and two paternal cousins. Mother carried homozygous deletion (indicated with an asterisk). Index’s daughter was tested to be negative for the deletion. Additionally, deleterious <i>BRCA1</i> c.5095C>T variant has been previously identified in three individuals in the family. Females are marked with circles and males are marked with squares. Index individual is marked with an arrow. Breast and ovarian cancers are marked with black circles with the age at diagnosis. Other cancers are marked with grey and specified with the age at diagnosis (Br: breast, Co: colon, Kid: kidney, Mel: melanoma, Ov: ovarian, To: tongue, Ute: uterus). Deceased individuals are marked with a slash. Current age of index’s healthy sister is indicated. Generations are marked with the Roman numerals on the left. The pedigree figure has been modified from Kuusisto <i>et al</i>, 2011 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071802#pone.0071802-Kuusisto1" target="_blank">[18]</a>.</p