Tracing Cell Fates in Human Colorectal Tumors from Somatic Microsatellite Mutations : Evidence of Adenomas with Stem Cell Architecture

Occult aspects of tumor proliferation are likely recorded genetically as their microsatellite (MS) loci become polymorphic. However, MS mutations generated by division may also be eliminated with death as noncoding MS loci lack selective value. Therefore, highly polymorphic MS loci cannot exist unless mutation rates are high, or unless mutation losses are inherently minimized. Mutations accumulate differently when cell fates are determined intrinsically before or extrinsically after division. Stem cell (asymmetrical division as in intestinal crypts) and random (asymmetrical and symmetrical division) proliferation, respectively, represent simulated cell fates determined before or after division. Whereas mutations regardless of selection systematically persist once inherited with stem cell proliferation, mutations are eliminated by the symmetrical losses of both daughter cells with random proliferation. Therefore, greater genetic diversity or MS variance accumulate with stem cell compared with random proliferation. MS loci in normal murine intestinal mucosa and xenografts of cancer cell lines accumulated mutations, respectively, consistent with stem cell and random proliferation. Tumors from patients with hereditary nonpolyposis colorectal cancer (HNPCC) demonstrated polymorphic MS loci. Overall, three of five adenomas and one of six cancers exhibited high MS variances. Assuming mutation rates are not significantly greater in adenomas than in cancers, these studies suggest the stem cell proliferation and hierarchy of normal intestines persists in many HNPCC adenomas and some cancers. An adenoma stem cell architecture can explain the complex polymorphic MS loci observed in HNPCC adenomas and account for many adenoma features. In contrast, cancers may lose intrinsic control of cell fate. These studies illustrate a feasible phylogenetic approach to unravel and describe occult aspects of human tumor proliferation. The switch from predominantly stem cell to random proliferation may be a critical and defining characteristic of malignancy.     

Germline hMSH2 and differential somatic mutations in patients with Turcot's syndrome.

Turcot's syndrome is characterized clinically by the occurrence of primary brain tumor and colorectal tumor and has in previous reports been shown to be associated with germline mutations in the genes APC, hMLH1, and hPMS2. Here we describe three patients with Turcot's syndrome, each having colorectal adenocarcinoma and malignant glioma. All the colorectal and brain tumors from these patients showed replication errors in most of the microsatellite loci investigated. Search for underlying germline mutations in the nucleotide mismatch repair genes revealed three different hMSH2 mutations. All colorectal tumors showed a frameshift in the A(10) tract in the coding sequence of the transforming growth factor beta type II receptor (TGFBRII) gene, but no such change was detected in any of the brain tumors. Frameshift mutation in the BAX gene was found in one colon carcinoma and mutations in insulin-like growth factor type II receptor (IGFIIR) gene in one glioma. Our data have broadened the possible mutation spectrum of patients with Turcot's syndrome. The difference in the mutation spectrum of TGFBRII, BAX, and IGFIIR between brain and colorectal tumors in these individuals suggests that the mutator phenotype may target different pathogenic pathways in the oncogenic process of the two organs.     

Mutator phenotype in cancer: timing and perspectives

Normal human cells replicate their DNA with exceptional accuracy. During every division cycle, each daughter cell receives a full and accurate complement of genetic information. It has been estimated that approximately one error occurs during DNA replication for each 10(9) to 10(10) nucleotides polymerized. Stem cells, the cells that are progenitors of cancer, may replicate their genes even more accurately. In contrast, the malignant cells that constitute a tumor are markedly heterogeneous and exhibit multiple chromosomal abnormalities and alterations in the nucleotide sequence of DNA. To account for the disparity between the rarity of mutations in normal cells and the large numbers of mutations present in cancer, we initially hypothesized that during tumor progression, cancer cells must exhibit a mutator phenotype. In this perspective, we summarize the evidence supporting a mutator phenotype in human cancer, analyze recent measurements of mutations in human cancer, consider the timing for the expression of a mutator phenotype, and focus on the important consequences of large numbers of random mutations in human tumors.     

Telomerase activity is commonly detected in hereditary nonpolyposis colorectal cancers.

Telomerase activity can be detected in most human cancers. These findings are consistent with the telomere hypothesis, which predicts telomerase expression after a number of mitotic divisions to prevent the progressive and catastrophic loss of telomeres. However, telomerase is not detected in a minority of colorectal cancers suggesting either alternative mechanisms of immortalization or that their telomeres have not yet shortened sufficiently to require telomerase activity. Colorectal cancers arising in patients with hereditary nonpolyposis colorectal cancer (HNPCC) were examined for telomerase activity because compared to sporadic tumors, HNPCC tumors are less likely to pass a telomere threshold as they occur in younger patients and exhibit "accelerated" progression, perhaps because of their characteristic mutator phenotypes and losses of mismatch repair. Primary, colorectal cancers, 13 in HNPCC patients, and 37 sporadic tumors (17 with mutator phenotypes) were examined for telomerase activity by the TRAP (telomeric repeat amplification protocol) assay. The majority of colorectal cancers contained detectable telomerase activity regardless of underlying phenotype (77 percent of HNPCC; 81 percent of sporadic tumors, 88 percent with mutator phenotypes and 75 percent without mutator phenotypes). Therefore, telomerase expression appears to be commonly acquired in the progression of both mutator phenotype and sporadic colorectal cancers.     

Cytogenetic aberrations and heterogeneity of mutations in repeat-containing genes in a colon carcinoma from a patient with hereditary nonpolyposis colorectal cancer

The majority of tumors from patients affected by hereditary nonpolyposis colorectal cancer (HNPCC) exhibit a mutator phenotype characterized by widespread microsatellite instability (MSI) and somatic mutations in repeated sequences in several cancer-associated genes. An inverse relationship between MSI and chromosomal instability (CIN) has been demonstrated and HNPCC-associated tumors are generally characterized by diploid or near-diploid cells with few or no chromosomal rearrangements. We have studied MSI, somatic mutations in repeat-containing genes, DNA-ploidy, and cytogenetic aberrations in a colon carcinoma from a patient with a germline MLH1 mutation. Mutations in coding repeats were assessed in 10 macroscopically separate areas of the primary tumor and in two lymph nodes. Some of the genes studied (E2F4, MSH3, MSH6, TCF4, and TGFBRII) showed a consistent lack of mutations, whereas others (BAX, Caspase-5 and IGFIIR) displayed alterations in some tumor regions but not in others. The tumor had DNA-index 1.1-1.2 and a stable, aberrant karyotype with extra copies of chromosomes 7 and 12 and the structural aberrations i(1q), der(20)t(8;20), and der(22)t(1;22). The finding of CIN, MSI, and somatic mutations in coding repeats in this tumor suggests that these phenomena may act together in HNPCC tumorigenesis. Furthermore, the observed intratumoral heterogeneity of mutations in coding repeats implies these changes occur late in tumorigenesis and, thus, probably play a role in tumor progression rather than initiation.     

Differences in the spectrum of spontaneous mutations in the hprt gene between tumor cells of the microsatellite mutator phenotype

We have determined the frequency and spectrum of spontaneous mutations at the hprt locus in LovO, HCT116, LS180 and DLD-1 colon carcinoma cell lines exhibiting microsatellite genetic instability. Each cell line has a different mutator gene. LoVo and HCT116 cells have mutated hMSH2 and hMLH1 genes, respectively, which account for the majority of hereditary non-polyposis colorectal cancer (HNPCC). LS180 cells are wild type for these genes and also for hPMS1 and hPMS2 mismatch repair genes. DLD-1 cells harbor a mutated GTBP mismatch binding factor and a mutated DNA Polymerase δ. The mutation rate at the hprt locus was several hundred fold higher in these cell lines relative to control cell lines without microsatellite instability. The mutations were frameshifts (deletions and insertions of a single nucleotide in short repeats) and single base substitutions (transversions and transitions). Some mutations were shared by these fouor cell lines. However, every cell line also exhibited a distinctive spectrum of mutations suggesting that each mutator gene induces a particular mutator phenotype. These results also suggest that the frequency and spectrum of somatic mutations in tumor cells of the microsatellite mutator phenotype may have diagnostic applications to discriminate among the diverse underlying mutator genes.     

Significance of mutations in TGFBR2 and BAX in neoplastic progression and patient outcome in sporadic colorectal tumors with high-frequency microsatellite instability

The mutator pathway implied in the development of colorectal cancer is characterized by microsatellite instability (MSI), which is determined by alterations of mismatch repair (MMR) genes. Defects in MMR genes affect repetitive DNA tracts interspersed mostly between coding sequences, and therefore it cannot be expected that they play a role during tumor progression. Genes containing repetitive sequences within their coding regions could be targets for MSI tumorigenesis, but this does not necessarily imply a causal role for the affected gene, because most are probably passenger mutations. We analyzed MSI and TGFBR2 and BAX frameshift mutations to further clarify the relationships between inactivation of the two genes and genomic instability in sporadic colorectal cancer (CRC), and to address how mutations in these genes influence the development of tumors and, eventually, patient outcome. One hundred and fifty-five patients with sporadic CRC were classified according to their MSI status. Frameshift mutations in the two genes were recurrent in high-frequency MSI (MSI-H) tumors, but these tended to be more common in poorly differentiated tumors. A high rate of mutations of TGFBR2 was found in tumors at Dukes' B stage, showing a greater extent of vascular invasion. Finally, in MSI-H tumors, mutations of either gene were associated with a significant decrease in survival. Our results contribute to the understanding of how the TGFBR2 and BAX gene mutations contribute to tumor progression in the mutator phenotype pathway for MSI colorectal cancers.     

Colorectal Adenoma and Cancer Divergence : Evidence of Multilineage Progression

Colorectal cancer progression involves changes in phenotype and genotype. Although usually illustrated as a linear process, more complex underlying pathways have not been excluded. The object of this paper is to apply modern quantitative principles of molecular evolution to multistep tumor progression. To reconstruct progression lineages, the genotypes of two adjacent adenoma-cancer pairs were determined by serial dilution and polymerase chain reaction at 28-30 microsatellite (MS) loci and then traced back to their most recent common ancestor. The tumors were mismatch repair deficient, and therefore relatively large numbers of MS mutations should accumulate during progression. As expected, the MS genotypes were similar (correlation coefficients >0.9) between different parts of the same adenoma or cancer, but very different (correlation coefficients <0. 2) between unrelated metachronous adenoma-cancer pairs. Unexpectedly, the genotypes of the adjacent adenoma-cancer pairs were also very different (correlation coefficients of 0.30 and 0.36), consistent with early adenoma-cancer divergence rather than direct linear progression. More than 60% of the divisions occurred after this early adenoma-cancer divergence. Therefore, the tumor phylogenies were not consistent with sequential stepwise selection along a single most "fit" and frequent lineage from adenoma to cancer. Instead, one effective early progression strategy creates and maintains multiple evolving candidate lineages, which are subsequently selected for terminal clonal expansion.     

c-k-ras and p53 mutations occur very early in adenocarcinoma of the lung.

The topographical distribution of a mutation provides insight into past patterns of tumor evolution. This approach was applied to two loci commonly mutated in adenocarcinoma of the lung--p53 and c-K-ras. In 41 primary adenocarcinomas, c-K-ras codon 12 point mutations were detected in 8 (19.5%) tumors and p53 point mutations were detected in 10 (24.4%) tumors, with one tumor harboring both mutations. These mutations were only detected in malignant cells and with a homogeneous topographical distribution throughout 16 tumors, including metastasis. Intratumor heterogeneity was detected in only one tumor in which a small portion lacked the specific p53 mutation. Based on this topographical analysis, it is likely that when these mutations occur in adenocarcinoma of the lung, they are usually acquired during the very earliest phases of tumor formation before the bulk of clonal expansion, and in very small precursor lesions.     

Activation-induced cytidine deaminase fails to induce a mutator phenotype in the human pre-B cell line Nalm-6

Activation-induced cytidine deaminase (AID) plays a key role in the induction of somatic hypermutation and class switching at the immunoglobulin loci of B lymphocytes. AID overexpression can induce a mutator phenotype in lymphoid and nonlymphoid cell lines, suggesting that AID by itself is sufficient to trigger hypermutation and class switching. AID expression in vivo is considered to be restricted to germinal center B lymphocytes, yet AID expression is also seen in many B cell lymphomas, hinting at a potential role for the development of these malignancies. We used a GFP-based reversion assay to efficiently evaluate the activation of mutator phenotypes. As expected, AID overexpression in the human Burkitt lymphoma cell line BL70 caused hypermutation. Surprisingly, AID overexpression in the human pre-B cell line Nalm-6 failed to induce a detectable mutator phenotype, indicating that Nalm-6 cells are probably lacking an essential factor(s) to confer AID-induced mutagenesis. This finding supports the concept that AID overexpression by itself must not automatically lead to the onset of a mutator phenotype. In addition, treating Nalm-6 transfectants with thymidine, a potential mutagenic drug, caused profound mutation rates on the GFP transgene. Thus, the GFP-based mutation assay might prove a powerful tool to study protein- and chemical-induced mutator phenotypes in cell lines.     

Low levels of microsatellite instability characterize MLH1 and MSH2 HNPCC carriers before tumor diagnosis

Microsatellite instability (MSI) characterizes tumors arising in patients with hereditary non-polyposis colorectal cancer (HNPCC) syndrome. HNPCC is a hereditary autosomal dominant disease caused by germline mutations in genes from the DNA (MMR) mismatch repair system. In these tumors, the loss of MMR compromises the genome integrity, allowing the progressive accumulation of mutations and the establishment of a mutator phenotype in a recessive manner. It is not clear, however, whether MSI can be detected in HNPCC carriers before tumor diagnosis. The aim of this study was to evaluate the presence of genetic instability in MMR gene carriers in peripheral blood lymphocytes of carriers and non-carriers members of two HNPCC families harboring a germline MLH1 and MSH2 mutation, respectively. An extensive analysis of the allelic distribution of single molecules of the polyA tract bat26 was performed using a highly sensitive PCR-cloning approach. In non-carriers, the allelic distribution of single bat26 molecules followed a gaussian distribution with no bat26 alleles shorter than (A)21. All mutation carriers showed unstable alleles [(A)20 or shorter] with an overall frequency of 5.6% (102/1814). We therefore suggest that low levels of genomic instability characterize MMR mutation carriers. These observations suggest that somatic mutations accumulate well before tumor diagnosis. Even though it is not clear whether this is due to the presence of a small percentage of cells with lost MMR or due to MMR haploinsufficiency, detection of these short unstable alleles might help in the identification of asymptomatic carriers belonging to families with no detectable MMR gene mutations.     

Biomaterial-induced sarcomagenesis is not associated with microsatellite instability

Sarcomagenesis, in contrast to carcinogenesis, is poorly understood. Microsatellite instability has been implicated in the development of many cancers, in particular those associated with chronic inflammatory conditions. In an experimental animal model, rats developed not only a peri-implantational chronic inflammatory reaction, but also malignant mesenchymal tumors in response to different biomaterials. Therefore, it was the aim of our study to test if the development of biomaterial-induced sarcomas is characterized by a mutator phenotype. A multiplex-PCR approach was designed to screen biomaterial-induced sarcomas for the presence of microsatellite instability. Seven different microsatellite loci were tested in ten tumors for microsatellite instability using a fluorochrome-labelled multiplex-PCR and subsequent fragment analysis. All tumors provided a microsatellite-stable phenotype at all loci tested. Our data suggest that microsatellite instability is rarely or not at all a feature of malignant transformation of biomaterial-induced soft tissue tumors. Thus, there is no evidence that a mutator phenotype is a hallmark of biomaterial-induced sarcomagenesis.     

Concurrent genetic alterations in DNA polymerase proofreading and mismatch repair in human colorectal cancer

Genomic sequences encoding the 3' exonuclease (proofreading) domains of both replicative DNA polymerases, pol delta and pol epsilon, were explored simultaneously in human colorectal carcinomas including six established cell lines. Three unequivocal sequence alterations, including one previously reported, were found, and all these were considered as dysfunctional mutations in light of the local amino-acid sequences. In particular, the F367S mutation found in the POLE gene encoding the pol epsilon catalytic subunit, which includes the proofreading domain, is the first found in human diseases. Surprisingly, the tumours carrying these proofreading domain mutations were all defective in DNA mismatch repair (MMR). In addition to the two cell lines with acknowledged MMR gene mutations, the third tumour was also demonstrated to harbour a distinct mutation in MLH1, and indeed exhibited a microsatellite-unstable phenotype. These findings suggest that, in concert with MMR deficiency, defective polymerase proofreading may also contribute to the mutator phenotype observed in human colorectal cancer. Our observations may suggest previously unrecognised complexities in the molecular abnormalities underlying the mutator phenotype in human neoplasms.     

Heterozygous Aprt mouse model: detection and study of a broad range of autosomal somatic mutations in vivo.

During the development of cancer a series of specific genetic alterations have to occur in a stepwise fashion to transform a normal somatic cell into a malignant tumor cell. These genetic changes can be roughly divided in two groups: mutations in proto-oncogenes that result in a constantly activated gene product and mutations in tumor-suppressor genes that result in loss of function. While oncogenic mutations often have a dominant phenotype and mutation of one allele is sufficient for activation, in general both alleles of a tumor suppressor gene have to be disrupted to abolish its function. The requested specificity for activating mutations in proto-oncogenes is high, since only a limited number of mutations at specific sites result in an activated protein. In contrast, disruption of a tumor suppressor gene can be accomplished via various mechanisms. Familial cancers often contain a germline mutation in one allele of a tumor suppressor gene. In tumors, the second allele is then frequently lost by genetic alterations that also affect the heterozygous state of multiple loci adjacent to the tumor suppressor gene. Genetic events especially, such as mitotic recombination, chromosome loss and deletion, are frequently responsible for the loss of the functional allele of heterozygous mutant tumor suppressor genes. We generated an Aprt(+/-) mouse model that allows us to study in detail the nature of the alterations that lead to loss of the wild-type Aprt allele in somatic cells. These genetic changes are thought to be analogous to those occurring at autosomal tumour suppressor genes, where they may contribute to the development of cancer. Furthermore, this mouse model allows determination of the extent and mechanisms by which chemical carcinogens induce loss of heterozygosity and identification of the nature of the DNA adducts responsible.     

Pretumor progression: clonal evolution of human stem cell populations

Multistep carcinogenesis through sequential cycles of mutation and clonal succession is usually described as tumor progression, or the clonal evolution of tumor cell populations. However, many mutations found in cancers are also compatible with normal appearing phenotypes and therefore genetic progression may precede tumor progression. To better characterize such pretumor progression (mutations in the absence of visible phenotypic changes), a quantitative model was developed that postulates most oncogenic cancer mutations first accumulate in normal appearing colon crypt niche stem cells. Each crypt contains multiple stem cells, and random niche stem cell loss with replacement eventually leads to the loss of all stem cell lineages except one. This niche succession or crypt clonal evolution is similar to the clonal succession of tumor progression except it does not require selection or change visible phenotype. Mutations may sequentially accumulate during stem cell clonal evolution either through drift (passenger mutations) or selection. To determine the feasibility of pretumor progression, mutation rates sufficient to recreate the epidemiology of colorectal cancer were estimated. Pretumor progression may completely substitute for visible tumor progression because it is theoretically possible for all cancer mutations to first accumulate in normal appearing colon with normal replication fidelity. Elevated mutation rates or tumorigenesis may be unnecessary for early progression.     

Genetic alterations in a patient with Turcot's syndrome

Turcot's syndrome (TS) Is a rare disorder associated with the development of both brain and colon neoplasms. Because of the very low incidence of the disease, its molecular basis remains unclear. Presented is a TS case of a 30-year-old Japanese male with a histopathologically confirmed diagnosis of both brain tumor (glioblastoma multiforme) and colon tumor (well-differentiated adenocar-clnoma). Germline mutations of the p53 gene, somatic mutations of the Ki-ras, p53and APC genes, and microsatel-lite Instability (MSI) was examined using polymerase chain reaction (PCR)-slngle strand conformation polymorphism analysis, followed by PCR-dlrect sequencing, and sequencing after subclonlng. No germline mutations of the p53 gene were found. Somatic mutations of Kl-ras and APC genes were found in the colon adenocarcinoma but not in the brain tumor. No somatic mutation of the pS3 gene was present in either colon or brain tumors. Microsatellite Instability of both colon and brain tumors was positive in two of four loci. These results indicate that the colon tumor of the TS patient carries the Kl-ras and APC gene mutations. The finding of MSI in both the brain and the colon tumors may support the hypothesis that alterations of DNA repair genes are involved in the tumor development of the TS patient.     

Impact of mutant p53 functional properties on TP53 mutation patterns and tumor phenotype: lessons from recent developments in the IARC TP53 database

The tumor suppressor gene TP53 is frequently mutated in human cancers. More than 75% of all mutations are missense substitutions that have been extensively analyzed in various yeast and human cell assays. The International Agency for Research on Cancer (IARC) TP53 database (www-p53.iarc.fr) compiles all genetic variations that have been reported in TP53. Here, we present recent database developments that include new annotations on the functional properties of mutant proteins, and we perform a systematic analysis of the database to determine the functional properties that contribute to the occurrence of mutational "hotspots" in different cancer types and to the phenotype of tumors. This analysis showed that loss of transactivation capacity is a key factor for the selection of missense mutations, and that difference in mutation frequencies is closely related to nucleotide substitution rates along TP53 coding sequence. An interesting new finding is that in patients with an inherited missense mutation, the age at onset of tumors was related to the functional severity of the mutation, mutations with total loss of transactivation activity being associated with earlier cancer onset compared to mutations that retain partial transactivation capacity. Furthermore, 80% of the most common mutants show a capacity to exert dominant-negative effect (DNE) over wild-type p53, compared to only 45% of the less frequent mutants studied, suggesting that DNE may play a role in shaping mutation patterns. These results provide new insights into the factors that shape mutation patterns and influence mutation phenotype, which may have clinical interest.     

Patterns of genetic alterations in pancreatic cancer: a pooled analysis

Both K-ras and p53 gene mutations are found commonly in pancreatic tumors. Analysis of the mutational patterns may provide insight into disease etiology. To further describe the mutational patterns of pancreatic cancer and to assess the evidence to date, we performed a pooled analysis of the published data on genetic mutations associated with pancreatic ductal adenocarcinoma. We included data from studies that evaluated point mutations in the two genes most studied in pancreatic cancer, K-ras and p53. A majority of the 204 tumors had mutations in at least one gene, with 29% having both K-ras and p53 mutations, 39% with K-ras mutation alone, and 16% having p53 mutation alone. Sixteen percent of tumors lacked mutation in either gene. K-ras mutations were present in high frequencies in all tumor grades (>69%). A statistically significant trend was observed for p53 mutation with higher tumor grade (P = 0.04). For K-ras, G2 and G3 grades, combined, had notably higher prevalences of mutation than G1 (P = 0.004). CGT mutations in K-ras codon 12 were marginally associated with lower tumor grade (P for trend = 0.09), and these tumors were somewhat less likely to have a p53 mutation than tumors with other K-ras mutations (P = 0.06). In the 59 K-ras+/p53+ tumors, 64% had the same type of mutation (transition or transversion) in both genes, suggesting a common mechanism. The mutational pattern of p53 in pancreatic cancer is similar to bladder cancer, another smoking-related cancer, but not to lung cancer. Analyses of molecular data, such as that performed here, present new avenues for epidemiologists in the study of the etiology of specific cancers.     

rolA locus of the Ri plasmid directs developmental abnormalities in transgenic tobacco plants

Plants containing the left T-DNA (TL) of Agrobacterium rhizogenes show a variety of developmental abnormalities that include severely wrinkled leaves, loss of apical dominance, reduced geotropism of roots, reduced internode distances, and floral hyperstyly. The TL-DNA also affects the morphology of tumor tissue at the site of inoculation on Kalanchoe diagremontiana leaves. Single mutations at four loci of the TL-DNA (rolA, rolB, rolC, and rolD) are known to affect tumor morphology on K. diagremontiana leaves. We regenerated plants from tissues transformed with TL-DNA containing mutations in each of the rol loci in order to determine which of the rol loci, if any, control the abnormal plant phenotype. Only plants regenerated after infection with bacteria containing a mutation in rolA locus showed loss of the wrinkled leaf phenotype. The rolA locus was cloned into the plant transformation vector pGA472 and introduced alone into plants. Transgenic plants containing rolA displayed the abnormal phenotype. These results indicate that rolA is the primary determinant of the severely wrinkled phenotype of Ri plasmid transgenic plants. Other rol loci may influence the degree of developmental abnormalities.     

Combined tumor genomic profiling and exome sequencing in a breast cancer family implicates ATM in tumorigenesis: A proof of principle study

Familial breast cancers (BCs) account for 10%‐20% of all diagnosed BCs, yet only 20% of such tumors arise in the context of a germline mutation in known tumor suppressor genes such as BRCA1 or BRCA2. The vast genetic heterogeneity which characterizes non BRCA1 and non BRCA2 (or BRCAx) families makes grouped studies impossible to perform. Next generation sequencing techniques, however, allow individual families to be studied to identify rare and or private mutations but the high number of genetic variants identified need to be sorted using pathogenicity or recurrence criteria. An additional sorting criterion may be represented by the identification of candidate regions defined by tumor genomic rearrangements. Indeed, comparative genomic hybridization (CGH) using single nucleotide polymorphism (SNP) arrays allows the detection of conserved ancestral haplotypes within recurrent regions of loss of heterozygosity, common to several familial tumors, which can highlight genomic loci harboring a germline mutation in cancer predisposition genes. The combination of both exome sequencing and SNP array‐CGH for a series of familial BC revealed a germline ATM mutation associated with a loss of the wild‐type allele in two BC from a BRCAx family. The analysis of additional breast tumors from ten BC families in which a germline ATM mutation had been identified revealed a high frequency of wild‐type allele loss. This result argues strongly in favor of the involvement of ATM in these tumors as a tumor suppressor gene and confirms that germline ATM mutations are involved in a subset of familial BC.