Chromosome Arm Level Research Articles

Abstract P2-07-06: Cumulative copy number imbalances after neoadjuvant chemotherapy residual breast tumor is an independent predictor of relapse

Abstract Background: Identifying breast cancer patients after neoadjuvant chemotherapy (NAC) at greatest risk of recurrence would enhance selection of patients who may benefit from novel adjuvant treatments. Patients. 243 stage I-III breast cancer patients who underwent NAC with ≥10% residual tumor cellularity were identified from the MD Anderson Cancer Center and Ben Taub General Hospital, Harris County hospital. Tumor DNA was isolated for DNA copy number using OncoScan CNV FFPE, Affymetrix. Median follow-up was 67.8 months. Continuous residual cancer burden (RCB) scores with CNI data were available for 152 cases. To test if CNIs covering large regions were associated with recurrence after adjusting for prognostic variables and study site, data were summed to a chromosome-arm level. Eleven chromosome arms with false discovery rate <0.05 for breast cancer recurrence were identified. A stepwise multivariable model including age at diagnosis, tumor subtype, histologic grade, pre- and post-treatment stage, study site, and the 11 chromosomal arms were used to fit a parsimonious multivariate model for recurrence. Minimizing the Akaike Information Criterion yielded a final model with post-stage and a 5-arm CNI (5A-CNI) indicator including 2q, 3q, 4q, 10p, and 18p. Tumors were classified on 5A-CNI as 0 [no CNI], 1 [1- 2] and 2 [> 2]. Results. The study population included 76 non-Hispanic White, 89 Hispanic, and 68 African American patients with a mean age of 49.1 years. 105 patients were classified as 5A-CNI-0, 97 as 5A-CNI-1 and 41 as 5A-CNI-2. A higher 5A-CNI score was associated with tumor grade, ER-negative tumors (p<0.002) and tumor subtype (p=0.014). For 5A-CNI scores of 0, 1 and 2, recurrence rates of 14%, 34% and 58.5% were observed, respectively. In the final multivariable model adjusted for post-stage, RCB and study site, when compared to 5A-CNI-0, the hazard of recurrence was elevated for 5A-CNI-1 (HR= 2.27 [95% CI, 1.01-5.1]) and 5A-CNI-2 tumors (HR=7.43 [95% CI, 2.85-19.39]). Further, while the sample size is limiting, of 10 patients who were RCB3 and 5A-CNI-2, 9 relapsed (90%) during follow-up compared to only 6 of 43 (14%) of RCB3 patients with 5A-CNI-0 (p<10-6). For patients with RCB1 or 2, relapse did not differ by 5A-CNI score. Neither race nor ethnicity were found to be independently associated with recurrence or tumor subtype. However, African American, followed by Hispanic patients, were more likely than non-Hispanic White patients to be classified as 5A-CNI-2 (p=0.013). Table 1.Significant difference in distribution of 5 arm CNI classifier by Race/Ethnicity in Study Sample (p =0.013).5A-CNI012Non-Hispanic Whiten=44; 57.9%n=25; 32.9%n=7; 9.2%Hispanicn=32; 36%n=42; 47.2%n=15; 16.9%African Americann=28; 41.2%n=23; 33.8%n=17; 25% Conclusion. The 5A-CNI score in post NAC tumor identifies a patient population with very poor prognosis independent of current clinical prognostic factors including RCB. Validation of these findings may lead to a post NAC genomic test that identifies patients who would benefit from additional treatment Further investigation of the nature of the association between the 5A-CNI score and race/ethnicity, which appears independent of tumor subtype, is warranted. Citation Format: Thompson PA, Brewster A, Tsavachidis S, Armstrong G, Do K-A, Ha M-J, Gutierrez C, Symmans F, Bondy M. Cumulative copy number imbalances after neoadjuvant chemotherapy residual breast tumor is an independent predictor of relapse [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-07-06.

A Next-Generation Sequencing-Based Karyotyping Algorithm Reveals the Genomic Structure of Acute Myeloid Leukemia

Introduction: The BeatAML master trial is evaluating the use of precision medicine via genomically guided therapy in acute myeloid leukemia (AML). A variety of assays are used to test patient samples including cytogenetic karyotyping, fluorescence in situ hybridization (FISH), and next-generation sequencing (NGS)-based approaches to analyze genomic alterations. We developed an algorithm to extract karyotype information from NGS-based genomic sequencing data in the BeatAML cohort. We also utilized this algorithm to retrospectively study 1603 unique AML samples collected during routine clinical care.Methods: Comprehensive genomic profiling (CGP) was performed using a CLIA/CAP/NYS approved DNA and RNA hybrid capture-based next-generation sequencing assay that sequences 426 genes in DNA and 265 genes to capture fusions by RNA. We analyzed aneuploidy by comparing the log ratio of read counts in tumor DNA to a process matched normal control and developed signal to noise metrics to measure chromosome arm copy number. A chromosome arm was considered altered if >50% of the arm was altered. Chromosome (chr) 5q was also considered lost if only chr5q31 (containing EGR1) was lost. Based on the noise metrics of each sample, we also calculated a per sample limit of detection, which was defined as the lowest percentage of cells that could have a single copy gain or loss and be detected. We validated chr5q loss, chr7q loss, and chr8 gain using FISH results obtained from available BeatAML samples as the gold standard. To better understand the genomic landscape of AML, we also included 1603 samples run in standard clinical practice. False discovery rate (FDR) was assessed using the Bonferroni method.Results: We developed a method to analyze chr5q loss, chr7q loss and chr8 gain that had 95% concordance across all chromosomes compared to the FISH gold standard. The median limit of detection was 10.1% (percentage of cells required to have a single copy gain/loss to be detected). Overall concordance adjusted for limit of detection was 97% with 92% sensitivity (55/60 chromosomes) and 99% specificity (162/164 chromosomes) with similar performance across chromosomes. For chr7q loss and chr8 gain, over 50% of the chromosomal region was altered. However, the size of the loss on chr5q varied widely from the entire arm to a single gene (EGR1). We next applied the algorithm to 1603 unique patient samples analyzed by CGP during routine clinical care. We detected loss of chr5q in 10.9% (174), loss of chr7q in 10.4% (166), and gain of chr8 in 9.2% (147) of AML samples. Frequently altered genes in this cohort included FLT3 (21%, 337), RUNX1 (20.5%, 328), DNMT3A (17.5% 280), and TP53 (17.5%, 280). To further explore the genomic landscape, we analyzed the cooccurrence of each chromosomal alteration with all genes assayed. All three chromosomal aberrations exhibited significant cooccurrence with each other and TP53 (FDR P < 0.05). TP53 was altered in 75% (130/174) of chr5q loss samples 49% (82/166) of chr7q loss samples and 37% (55/147) of chr8 gain samples. Loss of chr5q also exhibited significant mutual exclusivities with FLT3, DNMT3A, NPM1, SRSF2, ASXL1, CEBPA, and WT1 (FDR P < 0.05). Loss of chr7q exhibited a slightly different mutual exclusivity profile with FLT3, NPM1, and PTPN11 (FDR P < 0.05). The difference in the cooccurrence profile between chr5q and chr7q was not a matter of p-value cutoffs since the magnitude of effect varied widely between groups.Conclusions: We demonstrated an NGS-based algorithm to determine karyotype that has a high concordance with FISH results. Limit of detection was equivalent to karyotyping by metaphase analysis but slightly worse than FISH assays on freshly prepared samples. We identified a previously described genomic stratification of TP53-aneuploidy since chromosomal aberrations and TP53 exhibited significant cooccurrence. However, only 50% of samples with loss of chr5q exhibited loss of chr7q and vice versa. While both were mutually exclusive with FLT3 and NPM1, loss of chr5q was mutually exclusive with several genes of prognostic significance including chromatin factors (DNMT3A) and splice factors (SRSF2). This study shows how NGS-based approaches can capture both chromosome arm level copy number alterations as well as all four categories of genomic alterations, thereby enabling risk stratification and identification of potential treatment options as defined in current NCCN guidelines. DisclosuresPavlick:Foundation Medicine Inc: Employment. Montesion:Foundation Medicine Inc: Employment. Severson:Foundation Medicine Inc: Employment. Brennan:Foundation Medicine Inc: Employment. Frampton:Foundation Medicine Inc: Employment, Other: Employee and stockholder. He:Foundation Medicine Inc: Employment. Levine:Roche: Consultancy, Research Funding; Epizyme: Patents & Royalties; Celgene: Consultancy, Research Funding; Isoplexis: Equity Ownership; Prelude: Research Funding; Qiagen: Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Gilead: Honoraria; Janssen: Consultancy, Honoraria; Novartis: Consultancy; C4 Therapeutics: Equity Ownership; Imago: Equity Ownership; Loxo: Consultancy, Equity Ownership. Vergilio:Foundation Medicine Inc: Employment. Albacker:Foundation Medicine Inc: Employment; Foundation Medicine Inc: Employment.

Abstract P2-07-05: Genomic lesions and PD-1/PD-L1 expression in resected triple negative breast cancers

Abstract Introduction: Striking clinical responses to immunotherapies in subsets of patients with a variety of solid tumors have prompted the search for predictive biomarkers. Recent studies have proposed that gene specific and genome wide mutation and copy number signatures in tumor cells may be predictive of responses to immune checkpoint blockade. Notably high levels of PD-L1 on tumor cells, a context associated with an adaptive immune response, has been linked to specific oncogenic driver lesions including loss of PTEN, activating KRAS mutation, and MYC amplification, and to the total burden of copy number variants (CNVs) in aneuploid tumors. Triple negative breast cancers (TNBCs) typically have multiple driver mutations and high levels of CNVs in their genomes. Thus there is significant interest in exploiting genomic data for the development of prognostic immunotherapy biomarkers for patients with TNBC. Study Design: We interrogated 62 well annotated surgical resections from patients with TNBC and assessed the associations of genomic lesions with expression of PD-1 and PDL-1 in tumor and non-tumor cells in each sample. We applied a systematic approach to rigorously interrogate the genomes of each TNBC sample. Tumor ploidy was initially measured with DNA content flow cytometry followed by sorting the nuclei of distinct diploid, tetraploid, and aneuploid cell populations from each TNBC. The next level of analysis measured genome wide copy number variants (CNV) with oligonucleotide arrays designed for CNV detection using purified (&amp;gt;95%) tumor populations. This enabled the discrimination and mapping of CNVs including single copy losses and gains, focal amplifications, and homozygous deletions across each TNBC genome. Finally we generated whole exome data in a subset of samples to increase the resolution within loci of interest and to incorporate mutations of individual genes into our genomic signatures. This combined approach provides high resolution measures of TNBC genomes from ploidy, whole chromosome and chromosome arm level CNVs, focal amplicons, breakpoints and homozygous deletions, to the level of gene specific indels and mutations. In parallel whole tissue samples were screened by IHC for PD-1 and PD-L1 using validated antibodies and established scoring methods for staining of tumor and non-tumor cells. Results and Conclusions: High levels of PD-1 and PD-L1 were detected in 5/60 (8.3%) and 16/60 (26.7%) evaluable cases with staining of PD-1 exclusively on non tumor cells, while PD-L1 was primarily on tumor cells; 15/16 (93.8%) cases. These data were then used to test the associations of individual recurring genomic lesions, and the extent and nature of chromosome aberrations on the expression patterns of PD-1 and PD-L1. Homozygous deletion of PTEN or activating mutation in PIK3CA did not correlate with increased expression of either immune checkpoint regulator in TNBC cells. Furthermore tumors with highly aberrant aneuploid genomes and distinct oncogenic drivers frequently express relatively low levels of both proteins suggesting an intrinsic escape from immunosurveillance. Citation Format: Barrett MT, Lenkiewicz E, Malasi S, Yearley JH, Annamalai L, McCullough AE, Anderson KS, Pockaj BA. Genomic lesions and PD-1/PD-L1 expression in resected triple negative breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-07-05.

Genome Engineering to Generate Models of Chromosome Arm-Level Aneuploidies in Lung Cancer

Genome Engineering to Generate Models of Chromosome Arm-Level Aneuploidies in Lung Cancer

Genomic evolution and chemoresistance in germ-cell tumours.

Germ-cell tumours (GCTs) are derived from germ cells and occur most frequently in the testes. GCTs are histologically heterogeneous and distinctly curable with chemotherapy. Gains of chromosome arm 12p and aneuploidy are nearly universal in GCTs, but specific somatic genomic features driving tumour initiation, chemosensitivity and progression are incompletely characterized. Here, using clinical whole-exome and transcriptome sequencing of precursor, primary (testicular and mediastinal) and chemoresistant metastatic human GCTs, we show that the primary somatic feature of GCTs is highly recurrent chromosome arm level amplifications and reciprocal deletions (reciprocal loss of heterozygosity), variations that are significantly enriched in GCTs compared to 19 other cancer types. These tumours also acquire KRAS mutations during the development from precursor to primary disease, and primary testicular GCTs (TGCTs) are uniformly wild type for TP53. In addition, by functional measurement of apoptotic signalling (BH3 profiling) of fresh tumour and adjacent tissue, we find that primary TGCTs have high mitochondrial priming that facilitates chemotherapy-induced apoptosis. Finally, by phylogenetic analysis of serial TGCTs that emerge with chemotherapy resistance, we show how TGCTs gain additional reciprocal loss of heterozygosity and that this is associated with loss of pluripotency markers (NANOG and POU5F1) in chemoresistant teratomas or transformed carcinomas. Our results demonstrate the distinct genomic features underlying the origins of this disease and associated with the chemosensitivity phenotype, as well as the rare progression to chemoresistance. These results identify the convergence of cancer genomics, mitochondrial priming and GCT evolution, and may provide insights into chemosensitivity and resistance in other cancers.

Abstract 121: Analysis and comparison of somatic copy number alterations in gastric cardia adenocarcinoma and gastric non-cardia adenocarcinoma

Abstract Gastric adenocarcinoma is one of the most common cancer type worldwide. Anatomically it may raise from the cardia or non-cardia part of the stomach and previous studies have shown differential susceptibilities loci and prognosis between gastric cardia adenocarcinoma (GCA) and gastric non-cardia adenocarcinoma (GNCA). To better understand the genomic alterations that drive gastric adenocarcinoma and to investigate the differences of genetic aberration between GCA and GNCA, we analyzed somatic copy-number aberrations in 205 gastric adenocarcinomas resected samples, including 114 GCAs and 91 GNCAs using Illumina Human OmniZhongHua BeadChips. We identified 49 significantly recurrent focal alterations in gastric adenocarcinoma. In addition to those previously reported in stomach cancer, several novel focal changes were also observed, including gain of 11p11.2, 6q23.3, 12p11.1, 5p15.33 and loss of 8p11.22, 9p22.2, 18q22.1, 15q21.2, 17q23.3. A few known or potential oncogenes such as TERT, MYB, and IRS2, were included in the focal amplified regions that were not reported in gastric cancer before. Also, a few potential tumor suppressors were seen in these focal loss regions, including DOK6, BRIP1 and NDST4. Especially, HDC, a gene involved in gastric acid secretory, was harbored in the newly identified focal loss region, 15q21.2. Three focal changes, loss of 20p12.1 (containing MACROD2), 6q26 (containing PARK2), and gain of 11p11.2 (containing CRY2), were identified to correlate to the post-surgery overall survival, which may deserve to be further investigated as the potential prognosis markers. Comparison of somatic copy number alternation patterns revealed that in chromosome arm level, 16p and 5q had distinct copy number status between GCA and GNCA samples. The frequencies of three novel focal changes were significantly different between GCA and GNCA. Furthermore, KRAS amplification, a well characterized gastric adenocarcinoma prognosis marker was associated with worse clinical outcome in GNCA, but not in GCA. Taken together, these results provided novel candidate oncogenes or tumor suppressors for gastric adenocarcinoma and different features in structural alterations between GCA and GNCA, which potentially inform novel opportunities for targeted therapeutic interventions. Citation Format: Manjiao Liu, Zhen Liu, Jian Bai, Hong Cai, Yang Ke, Changqing Zeng. Analysis and comparison of somatic copy number alterations in gastric cardia adenocarcinoma and gastric non-cardia adenocarcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 121.

Characterization of repetitive DNA landscape in wheat homeologous group 4 chromosomes.

BackgroundThe number and complexity of repetitive elements varies between species, being in general most represented in those with larger genomes. Combining the flow-sorted chromosome arms approach to genome analysis with second generation DNA sequencing technologies provides a unique opportunity to study the repetitive portion of each chromosome, enabling comparisons among them. Additionally, different sequencing approaches may produce different depth of insight to repeatome content and structure. In this work we analyze and characterize the repetitive sequences of Triticum aestivum cv. Chinese Spring homeologous group 4 chromosome arms, obtained through Roche 454 and Illumina sequencing technologies, hereinafter marked by subscripts 454 and I, respectively.Repetitive sequences were identified with the RepeatMasker software using the interspersed repeat database mips-REdat_v9.0p. The input sequences consisted of our 4DS454 and 4DL454 scaffolds and 4ASI, 4ALI, 4BSI, 4BLI, 4DSI and 4DLI contigs, downloaded from the International Wheat Genome Sequencing Consortium (IWGSC).ResultsRepetitive sequences content varied from 55% to 63% for all chromosome arm assemblies except for 4DLI, in which the repeat content was 38%. Transposable elements, small RNA, satellites, simple repeats and low complexity sequences were analyzed. SSR frequency was found one per 24 to 27 kb for all chromosome assemblies except 4DLI, where it was three times higher. Dinucleotides and trinucleotides were the most abundant SSR repeat units. (GA)n/(TC)n was the most abundant SSR except for 4DLI where the most frequently identified SSR was (CCG/CGG)n. Retrotransposons followed by DNA transposons were the most highly represented sequence repeats, mainly composed of CACTA/En-Spm and Gypsy superfamilies, respectively. This whole chromosome sequence analysis allowed identification of three new LTR retrotransposon families belonging to the Copia superfamily, one belonging to the Gypsy superfamily and two TRIM retrotransposon families. Their physical distribution in wheat genome was analyzed by fluorescent in situ hybridization (FISH) and one of them, the Carmen retrotransposon, was found specific for centromeric regions of all wheat chromosomes.ConclusionThe presented work is the first deep report of wheat repetitive sequences analyzed at the chromosome arm level, revealing the first insight into the repeatome of T. aestivum chromosomes of homeologous group 4.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1579-0) contains supplementary material, which is available to authorized users.

Inferring copy number and genotype in tumour exome data.

BackgroundUsing whole exome sequencing to predict aberrations in tumours is a cost effective alternative to whole genome sequencing, however is predominantly used for variant detection and infrequently utilised for detection of somatic copy number variation.ResultsWe propose a new method to infer copy number and genotypes using whole exome data from paired tumour/normal samples. Our algorithm uses two Hidden Markov Models to predict copy number and genotypes and computationally resolves polyploidy/aneuploidy, normal cell contamination and signal baseline shift. Our method makes explicit detection on chromosome arm level events, which are commonly found in tumour samples. The methods are combined into a package named ADTEx (Aberration Detection in Tumour Exome). We applied our algorithm to a cohort of 17 in-house generated and 18 TCGA paired ovarian cancer/normal exomes and evaluated the performance by comparing against the copy number variations and genotypes predicted using Affymetrix SNP 6.0 data of the same samples. Further, we carried out a comparison study to show that ADTEx outperformed its competitors in terms of precision and F-measure.ConclusionsOur proposed method, ADTEx, uses both depth of coverage ratios and B allele frequencies calculated from whole exome sequencing data, to predict copy number variations along with their genotypes. ADTEx is implemented as a user friendly software package using Python and R statistical language. Source code and sample data are freely available under GNU license (GPLv3) at http://adtex.sourceforge.net/.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-732) contains supplementary material, which is available to authorized users.

Abstract LB-314: Array comparative genomic hybridization of thymic epithelial tumors identifies loss of CDKN2A as a prognostic factor and BCL2 family members as targets for therapy

Abstract Background: Thymic epithelial tumors (TETs) are rare and the genomic aberrations relevant to TET biology are unknown. The goal of this study was to identify recurrent genomic aberrations in TETs. Materials and Methods: From a series of 132 TET resected patients we selected 59 formalin fixed paraffin embedded (FFPE) samples with more than 80% of cancer cells in order to perform high-resolution array-CGH. We used ULS labeling kit (Agilent) and 105A array (Agilent) for 20 and 180K array (Agilent) for 39 samples. For the immunohistochemistry we used a tissue micro-array built from FFPE samples of the 132 patients. The viability assay MTS (Promega) was used to evaluate cytotoxicity of Gx15–070 and ABT-263 (Selleck Chemicals) in T1889, TY82 and T1682 TET cell lines. Results: Chromosome arm level copy number (CN) aberrations were considered those chromosome arms with more than 80% of their length affected by either CN gain or loss. Rare non-recurrent chromosome arm-level CN aberrations were observed in type A thymomas, whereas types B3 and thymic carcinomas shared frequent gains of chromosomes 1q, 5 and 7, as well as losses of chromosomes 6 and 13q. In addition, thymic carcinomas presented frequent losses of chromosomes 16p and 17q. We applied the GISTIC algorithm to the whole set of CN aberrations in order to distinguish aberrations driving the cancer phenotype from the background level of random CN aberrations. 72 CN gain and 54 CN loss peaks were identified (q&amp;lt;0.25). Only two peaks were associated with a significant (p&amp;lt;0.05) poor disease related survival and time to progression. These two peaks represented one CN gain (log2 ratio &amp;gt; 0.3) containing BCL2 locus and one high-level CN loss (log2 ratio &amp;lt; −0.7) containing CDKN2A/B loci. None of the samples with CDKN2A CN loss (5/59) expressed the related proteins p16INK4 and p14ARF. Patients with CDKN2A-negative immunohistochemistry results (85/119) had a poorer disease related survival (LogRank p=0.041). TET cell lines did not have CDKN2A CN loss or BCL2 CN gain, none of them expressed CDKN2A proteins and T1682 and TY82 expressed BCL2. All TET cell lines expressed multiple BCL2 anti-apoptotic family members including MCL1, and were resistant to ABT-263, a BCL2, BCL-XL and BCL-W inhibitor, but sensitive to Gx15–070, a pan BCL2 anti-apoptotic family member (IC50: range 35.8–99.6 nM). Conclusion: Our data indicate that TET histotypes differ by distribution of chromosome arm level CN aberrations. Loss of CDKN2A is prognostic in TETs, whereas Bcl-2 family members may be valuable targets for treatment of this disease. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-314. doi:10.1158/1538-7445.AM2011-LB-314

RESTRICTED GENE FLOW AT SPECIFIC PARTS OF THE SHREW GENOME IN CHROMOSOMAL HYBRID ZONES

The species and races of the shrews of the Sorex araneus group exhibit a broad range of chromosomal polymorphisms. European taxa of this group are parapatric and form contact or hybrid zones that span an extraordinary variety of situations, ranging from absolute genetic isolation to almost free gene flow. This variety seems to depend for a large part on the chromosome composition of populations, which are primarily differentiated by various Robertsonian fusions of a subset of acrocentric chromosomes. Previous studies suggested that chromosomal rearrangements play a causative role in the speciation process. In such models, gene flow should be more restricted for markers on chromosomes involved in rearrangements than on chromosomes common in both parent species. In the present study, we address the possibility of such differential gene flow in the context of two genetically very similar but karyotypically different hybrid zones between species of the S. araneus group using microsatellite loci mapped to the chromosome arm level. Interspecific genetic structure across rearranged chromosomes was in general larger than across common chromosomes. However, the difference between the two classes of chromosomes was only significant in the hybrid zone where the complexity of hybrids is expected to be larger. These differences did not distinguish populations within species. Therefore, the rearranged chromosomes appear to affect the reproductive barrier between karyotypic species, although the strength of this effect depends on the complexity of the hybrids produced.

Chromosome localization of microsatellite markers in the shrews of the Sorex araneus group

The extremely high rate of karyotypic evolution that characterizes the shrews of the Sorex araneus group makes this group an exceptionally interesting model for population genetics and evolutionary studies. Here, we attempted to map 46 microsatellite markers at the chromosome arm level using flow-sorted chromosomes from three karyotypically different taxa of the Sorex araneus group (S. granarius and the chromosome races Cordon and Novosibirsk of S. araneus). The most likely localizations were provided for 35 markers, among which 25 were each unambiguously mapped to a single locus on the corresponding chromosomes in the three taxa, covering the three sexual chromosomes (XY1Y2) and nine of the 18 autosomal arms of the S. araneus group. The results provide further evidence for a high degree of conservation in genome organization in the S. araneus group despite the presence of numerous Robertsonian rearrangements. These markers can therefore be used to compare the genetic structure among taxa of the S. araneus group at the chromosome level and to study the role of chromosomal rearrangements in the genetic diversification and speciation process of this group.

RESTRICTED GENE FLOW AT SPECIFIC PARTS OF THE SHREW GENOME IN CHROMOSOMAL HYBRID ZONES

The species and races of the shrews of the Sorex araneus group exhibit a broad range of chromosomal polymorphisms. European taxa of this group are parapatric and form contact or hybrid zones that span an extraordinary variety of situations, ranging from absolute genetic isolation to almost free gene flow. This variety seems to depend for a large part on the chromosome composition of populations, which are primarily differentiated by various Robertsonian fusions of a subset of acrocentric chromosomes. Previous studies suggested that chromosomal rearrangements play a causative role in the speciation process. In such models, gene flow should be more restricted for markers on chromosomes involved in rearrangements than on chromosomes common in both parent species. In the present study, we address the possibility of such differential gene flow in the context of two genetically very similar but karyotypically different hybrid zones between species of the S. araneus group using microsatellite loci mapped to the chromosome arm level. Interspecific genetic structure across rearranged chromosomes was in general larger than across common chromosomes. However, the difference between the two classes of chromosomes was only significant in the hybrid zone where the complexity of hybrids is expected to be larger. These differences did not distinguish populations within species. Therefore, the rearranged chromosomes appear to affect the reproductive barrier between karyotypic species, although the strength of this effect depends on the complexity of the hybrids produced.