Interstitial chromosomal deletion of the tuberous sclerosis complex 2 locus is a signature for radiation-associated renal tumors in Eker rats

Ionizing radiation can damage DNA and, therefore, is a risk factor for cancer. Eker rats, which carry a heterozygous germline mutation in the tumor-suppressor gene tuberous sclerosis complex 2 (Tsc2), are susceptible to radiation-induced renal carcinogenesis. However, the molecular mechanisms involved in Tsc2 inactivation are unclear. We subjected Fischer 344 × Eker (Long Evans Tsc2+/- ) F1 hybrid rats to gamma-irradiation (2 Gy) at gestational day 19 (GD19) or postnatal day 5 (PND5) and investigated the patterns of genomic alterations in the Tsc2 allele of renal tumors that developed at 1 year after irradiation (N = 24 tumors for GD19, N = 10 for PND5), in comparison with spontaneously developed tumors (N = 8 tumors). Gamma-irradiation significantly increased the multiplicity of renal tumors. The frequency of LOH at the chromosome 10q12 region, including the Tsc2 locus, was 38%, 29% and 60% in renal carcinomas developed from the nonirradiated, GD19 and PND5 groups, respectively. Array comparative genomic hybridization analysis revealed that the LOH patterns on chromosome 10 in renal carcinomas were classified into chromosomal missegregation, mitotic recombination and chromosomal deletion types. LOH of the interstitial chromosomal deletion type was observed only in radiation-associated carcinomas. Sequence analysis for the wild-type Tsc2 allele in the LOH-negative carcinomas identified deletions (nonirradiated: 26%; GD19: 21%) and base-substitution mutations (GD19: 4%). Reduced expression of Tsc2 was also observed in the majority of the LOH-negative carcinomas. Our results suggest that interstitial chromosomal deletion is a characteristic mutagenic event caused by ionizing radiation, and it may contribute to the assessment of radiation-induced cancer risk.

[Genetic studies and neurodevelopment. From effectiveness to genetic models]

Advances in genetics have been able to support the clinical suspicion on the large hereditary component of most of these neurodevelopmental disorders (NDD). Initial studies on heritability, linkage or association showed from the beginning the great contribution of genotypic variation to the clinic in general, and to NDD in particular. The effectiveness of genetic studies in clinical practice, targeted to aetiological diagnosis, should not be ignored. Most of these are protocolized in the study of disorders such as intellectual disability and autism; within these, the array comparative genomic hybridization have supported a greater diagnostic effectiveness with respect to historical cytogenetic techniques (3 vs. 10% respectively). However, the irruption and success of molecular genetic sequencing techniques, particularly the exome and genome in trio, analyzing the parents (diagnostic rates of 30-50%), are conditioning the modification of the genetic algorithms in the diagnosis of different NDD. The greater knowledge of causal variants in intellectual disability and autism is also modifying the polygenic theoretical models established to date.

Prenatal diagnosis and molecular cytogenetic characterization of partial dup(18q)/del(18p) due to a paternal pericentric inversion 18 in a fetus with multiple anomalies

OBJECTIVE

We present prenatal diagnosis of rec(18)dup(18q)inv(18)(p11.2q21.2)pat owing to paternal pericentric inversion in a fetus.

CASE REPORT

A 37-year-old woman was diagnosed with multiple anomalies on a prenatal ultrasound scan at 17 weeks and 5 days of gestation. She underwent amniocentesis at 20 weeks and 2 days. Conventional karyotyping of amniocyte showed 46, XX, der(18). She was thus referred for genetic counseling; cytogenetic analysis revealed a 46, XY karyotype, inv(18)(p11.2q21.2), of the father. Therefore, based on the results of the father, the fetal karyotype was defined as 46, XX, rec(18)dup(18q)inv(18)(p11.2q21.2)pat. Array comparative genomic hybridization of amniocytes to obtain specific information showed a 3-Mb deletion of 18p11.31p11.32 (136227_3100353)x1 and a 23.7-Mb duplication of 18q21.31-q23 (54222717_77957375) × 3.

CONCLUSION

Maternal serum screening produces normal results for 18p-/18q+ syndrome, but it can be diagnosed by fluorescent in situ hybridization, quantitative-fluorescent polymerase chain reaction, or array comparative genomic hybridization test by observing abnormal findings on ultrasound.

Application of DArT seq derived SNP tags for comparative genome analysis in fishes; An alternative pipeline using sequence data from a non-traditional model species, Macquaria ambigua

Bi-allelic Single Nucleotide Polymorphism (SNP) markers are widely used in population genetic studies. In most studies, sequences either side of the SNPs remain unused, although these sequences contain information beyond that used in population genetic studies. In this study, we show how these sequence tags either side of a single nucleotide polymorphism can be used for comparative genome analysis. We used DArTseq (Diversity Array Technology) derived SNP data for a non-model Australian native freshwater fish, Macquaria ambigua, to identify genes linked to SNP associated sequence tags, and to discover homologies with evolutionarily conserved genes and genomic regions. We concatenated 6,776 SNP sequence tags to create a hypothetical genome (representing 0.1–0.3% of the actual genome), which we used to find sequence homologies with 12 model fish species using the Ensembl genome browser with stringent filtering parameters. We identified sequence homologies for 17 evolutionarily conserved genes (cd9b, plk2b, rhot1b, sh3pxd2aa, si:ch211-148f13.1, si:dkey-166d12.2, zgc:66447, atp8a2, clvs2, lyst, mkln1, mnd1, piga, pik3ca, plagl2, rnf6, sec63) along with an ancestral evolutionarily conserved syntenic block (euteleostomi Block_210). Our analysis also revealed repetitive sequences covering approximately 12% of the hypothetical genome where DNA transposon, LTR and non-LTR retrotransposons were most abundant. A hierarchical pattern of the number of sequence homologies with phylogenetically close species validated the approach for repeatability. This new approach of using SNP associated sequence tags for comparative genome analysis may provide insight into the genome evolution of non-model species where whole genome sequences are unavailable.

Clonality analysis of pulmonary tumors by genome-wide copy number profiling

Multiple tumors in patients are frequently diagnosed, either synchronous or metachronous. The distinction between a second primary and a metastasis is important for treatment. Chromosomal DNA copy number aberrations (CNA) patterns are highly unique to specific tumors. The aim of this study was to assess genome-wide CNA-patterns as method to identify clonally related tumors in a prospective cohort of patients with synchronous or metachronous tumors, with at least one intrapulmonary tumor. In total, 139 tumor pairs from 90 patients were examined: 35 synchronous and 104 metachronous pairs. Results of CNA were compared to histological type, clinicopathological methods (Martini-Melamed-classification (MM) and ACCP-2013-criteria), and, if available, EGFR- and KRAS-mutation analysis. CNA-results were clonal in 74 pairs (53%), non-clonal in 33 pairs (24%), and inconclusive in 32 pairs (23%). Histological similarity was found in 130 pairs (94%). Concordance between histology and conclusive CNA-results was 69% (74 of 107 pairs: 72 clonal and two non-clonal). In 31 of 103 pairs with similar histology, genetics revealed non-clonality. In two out of four pairs with non-matching histology, genetics revealed clonality. The subgroups of synchronous and metachronous pairs showed similar outcome for the comparison of histological versus CNA-results. MM-classification and ACCP-2013-criteria, applicable on 34 pairs, and CNA-results were concordant in 50% and 62% respectively. Concordance between mutation matching and conclusive CNA-results was 89% (8 of 9 pairs: six clonal and two non-clonal). Interestingly, in one patient both tumors had the same KRAS mutation, but the CNA result was non-clonal. In conclusion, although some concordance between histological comparison and CNA profiling is present, arguments exist to prefer extensive molecular testing to determine whether a second tumor is a metastasis or a second primary.

Subtelomeric Rearrangements: Presentation of 21 Probands with Emphasis on Familial Cases

INTRODUCTION

Intellectual disability affects 2% - 3% of the general population, with a chromosomal abnormality being found in 4% - 28% of these patients and a cryptic subtelomeric abnormality in 3% - 16%. In most cases, these subtelomeric rearrangements are submicroscopic, requiring techniques other than conventional karyotype for detection. They may be de novo or inherited from an affected parent or from a healthy carrier of a balanced chromosomal abnormality. The aim of this study was to characterize patients from our medical genetics center, in whom both a deletion and duplication in subtelomeric regions were found.

MATERIAL AND METHODS

Clinical and cytogenetic characterization of 21 probands followed at our center, from 1998 until 2017, with subtelomeric rearrangements.

RESULTS

There were 21 probands from 19 families presenting with intellectual disability and facial dysmorphisms. Seven had behavior changes, five had epilepsy and 14 presented with some other sign or symptom. Four had chromosomal abnormalities detected by conventional karyotype and four were diagnosed by array-comparative genomic hybridization. In four cases, parental studies were not possible. The online mendelian inheritance in man classification was provided whenever any of the phenotypes (deletion or duplication syndrome) was dominant.

DISCUSSION

Patients and relevant family members were clinically and cytogenetically characterized. Although rare, subtelomeric changes are a substantial cause of syndromic intellectual disability with important familial repercussions. It is essential to remember that a normal array-comparative genomic hybridization result does not exclude a balanced rearrangement in the parents.

CONCLUSION

Parental genetic studies are essential not only for a complete characterization of the rearrangement, but also for accurate genetic counselling and screening of family members at risk for recurrence.

Williams-Beuren syndrome in Mexican patients confirmed by FISH and assessed by aCGH

Williams-Beuren syndrome (WBS) has a prevalence of 1/7500-20000 live births and results principally from a de novo deletion in 7q11.23 with a length of 1.5 Mb or 1.8 Mb. This study aimed to determine the frequency of 7q11.23 deletion, size of the segment lost, and involved genes in 47 patients with a clinical diagnosis of WBS and analysed by fluorescence in situ hybridization (FISH); among them, 31 had the expected deletion. Micro-array comparative genomic hybridization (aCGH) confirmed the loss in all 18 positive-patients tested: 14 patients had a 1.5 Mb deletion with the same breakpoints at 7q11.23 (hg19: 72726578-74139390) and comprising 24 coding genes from TRIM50 to GTF2I. Four patients showed an atypical deletion: two had a 1.6 Mb loss encompassing 27 coding genes, from NSUN5 to GTF2IRD2; another had a 1.7 Mb deletion involving 27 coding genes, from POM121 to GTF2I; the remaining patient presented a deletion of 1.2 Mb that included 21 coding genes from POM121 to LIMK1. aCGH confirmed the lack of deletion in 5/16 negative-patients by FISH. All 47 patients had the characteristic facial phenotype of WBS and 45 of 47 had the typical behavioural and developmental abnormalities. Our observations further confirm that patients with a classical deletion present a typical WBS phenotype, whereas those with a high (criteria of the American Association of Pediatrics, APP) clinical score but lacking the expected deletion may harbour an ELN point mutation. Overall, the concomitant CNVs appeared to be incidental findings.

Comparative genomics and transcriptomics analysis reveals evolution patterns of selection in the Salix phylogeny

BACKGROUND

Willows are widely distributed in the northern hemisphere and have good adaptability to different living environment. The increasing of genome and transcriptome data provides a chance for comparative analysis to study the evolution patterns with the different origin and geographical distributions in the Salix phylogeny.

RESULTS

Transcript sequences of 10 Salicaceae species were downloaded from public databases. All pairwise of orthologues were identified by comparative analysis in these species, from which we constructed a phylogenetic tree and estimated the rate of diverse. Divergence times were estimated in the 10 Salicaceae using comparative transcriptomic analysis. All of the fast-evolving positive selection sequences were identified, and some cold-, drought-, light-, universal-, and heat- resistance genes were discovered.

CONCLUSIONS

The divergence time of subgenus Vetrix and Salix was about 17.6-16.0 Mya during the period of Middle Miocene Climate Transition (21-14 Mya). Subgenus Vetrix diverged to migratory and resident groups when the climate changed to the cool and dry trend by 14 Mya. Cold- and light- stress genes were involved in positive selection among the resident Vetrix, and which would help them to adapt the cooling stage. Universal- stress genes exhibited positive selection among the migratory group and subgenus Salix. These data are useful for comprehending the adaptive evolution and speciation in the Salix lineage.

Comparable Genomic Copy Number Aberrations Differ across Astrocytoma Malignancy Grades

A collection of intracranial astrocytomas of different malignancy grades was analyzed for copy number aberrations (CNA) in order to identify regions that are driving cancer pathogenesis. Astrocytomas were analyzed by Array Comparative Genomic Hybridization (aCGH) and bioinformatics utilizing a Bioconductor package, Genomic Identification of Significant Targets in Cancer (GISTIC) 2.0.23 and DAVID software. Altogether, 1438 CNA were found of which losses prevailed. On our total sample, significant deletions affected 14 chromosomal regions, out of which deletions at 17p13.2, 9p21.3, 13q12.11, 22q12.3 remained significant even at 0.05 q-value. When divided into malignancy groups, the regions identified as significantly deleted in high grades were: 9p21.3; 17p13.2; 10q24.2; 14q21.3; 1p36.11 and 13q12.11, while amplified were: 3q28; 12q13.3 and 21q22.3. Low grades comprised significant deletions at 3p14.3; 11p15.4; 15q15.1; 16q22.1; 20q11.22 and 22q12.3 indicating their involvement in early stages of tumorigenesis. Significantly enriched pathways were: PI3K-Akt, Cytokine-cytokine receptor, the nucleotide-binding oligomerization domain (NOD)–like receptor, Jak-STAT, retinoic acid-inducible gene (RIG)-I-like receptor and Toll-like receptor pathways. HPV and herpex simplex infection and inflammation pathways were also represented. The present study brings new data to astrocytoma research amplifying the wide spectrum of changes that could help us identify the regions critical for tumorigenesis.

Metacaspase gene family in Rosaceae genomes: Comparative genomic analysis and their expression during pear pollen tube and fruit development

Metacaspase (MC), which is discovered gene family with distant caspase homologs in plants, fungi, and protozoa, may be involved in programmed cell death (PCD) processes during plant development and respond abiotic and biotic stresses. To reveal the evolutionary relationship of MC gene family in Rosaceae genomes, we identified 8, 7, 8, 12, 12, and 23 MC genes in the genomes of Fragaria vesca, Prunus mume, Prunus persica, Pyrus communis, Pyrus bretschneideri and Malus domestica, respectively. Phylogenetic analysis suggested that the MC genes could be grouped into three clades: Type I*, Type I and Type II, which was supported by gene structure and conserved motif analysis. Microsynteny analysis revealed that MC genes present in the corresponding syntenic blocks of P. communis, P. bretschneideri and M. domestica, and further suggested that large-scale duplication events play an important role in the expansion of MC gene family members in these three genomes than other Rosaceae plants (F. vesca, P. mume and P. persica). RNA-seq data showed the specific expression patterns of PbMC genes in response to drought stress. The expression analysis of MC genes demonstrated that PbMC01 and PbMC03 were able to be detected in all four pear pollen tubes and seven fruit development stages. The current study highlighted the evolutionary relationship and duplication of the MC gene family in these six Rosaceae genomes and provided appropriate candidate genes for further studies in P. bretschneideri.

WaveDec: A Wavelet Approach to Identify Both Shared and Individual Patterns of Copy-Number Variations

Copy-number variations (CNVs) are associated with complex diseases and particular tumor types. Array-based comparative genomic hybridization (aCGH) is a common approach for the detection of CNVs. Traditional CNV detection methods for multiple aCGH samples mainly use batch samples to find common variations, not accounting for the individual characteristics of each sample. Accurately differentiating both the commonly shared and the individual CNV patterns is pivotal to identify cell populations, or to distinguish cell growth (as in cancer) from invasion of new cells. Our preliminary results have now demonstrated that both the shared and individual CNV patterns have distinctive characteristics after wavelet transform.

METHODS

To exploit these characteristics, we propose to formulate a quadratic data-separation problem within the wavelet space to discriminate the shared and individual CNVs from raw data. We have elaborated a numerical solution and shown that the solution can be obtained by solving decoupled subproblems. By this approach, computational costs can be limited, enabling efficient application in the analysis of large sequencing datasets.

RESULTS

The advantages of our proposed method, called WaveDec, have been demonstrated by comparison with popular CNV-detection methods using synthetic and empirical aCGH data. The performance of WaveDec was further validated by experiments with single-cell-sequencing data.

CONCLUSION

WaveDec can successfully differentiate shared and individual patterns, and performs well even in data contaminated with high levels of noise.

SIGNIFICANCE

Both the shared and individual patterns can be uniquely characterized as well as effectively decomposed within the wavelet space.

aCGH Analysis of Predictive Biomarkers for Response to Bevacizumab plus Oxaliplatin- or Irinotecan-Based Chemotherapy in Patients with Metastatic Colorectal Cancer

BACKGROUND

The randomized phase III study (WJOG4407G) showed equivalent efficacy between FOLFOX and FOLFIRI in combination with bevacizumab as the first-line treatment for metastatic colorectal cancer (mCRC). We studied whole genome copy number profiles using array-based comparative genomic hybridization (aCGH) analysis of tumor tissue samples obtained in this study. The aim of this study was to identify gene copy number alterations that could aid in selecting either FOLFOX or FOLFIRI in combination with bevacizumab for patients with mCRC.

MATERIALS AND METHODS

DNA was purified from 154 pretreatment formalin-fixed paraffin-embedded tissue samples (75 from the FOLFOX arm and 79 from the FOLFIRI arm) of 395 patients enrolled in the WJOG4407G trial and analyzed by aCGH. Genomic regions greater than 1.2-fold were regarded as copy number gain (CNG).

RESULTS

Patient characteristics between the treatment arms were well balanced except for tumor laterality (left side; 64% in FOLFOX arm and 80% in FOLFIRI arm, p = .07). FOLFIRI showed a trend toward better response rate (RR), progression-free survival (PFS) and overall survival (OS) than FOLFOX in the patients with CNG of chromosome 8q24.1 (Fisher's exact test, p = .134 for RR; interaction test, p = .102 for PFS and p = .003 for OS) and 8q24.2 (Fisher's exact test, p = .179 for RR; interaction test, p = .144 for PFS and p = .002 for OS).

CONCLUSION

Chromosome 8q24.1-q24.2 may contain genes that could potentially serve as predictive markers for selecting either FOLFOX or FOLFIRI in combination with bevacizumab for treatment of patients with mCRC.

IMPLICATIONS FOR PRACTICE

Bevacizumab has been used as a standard first-line treatment for patients with metastatic colorectal cancer (mCRC) in combination with either oxaliplatin-based or irinotecan-based chemotherapy. Until now, there has been no predictive marker to choose between the two combination chemotherapies. This array-based comparative genomic hybridization analysis revealed that the difference in therapeutic effect between the two combination chemotherapies is prominent in patients with mCRC with gene copy number gain in chromosome 8p24.1-p24.2. Such patients showed more favorable response and survival when treated with irinotecan-based combination chemotherapy. Overlapping genes commonly found in this region may be predictive biomarkers of the efficacy of the combination chemotherapy with bevacizumab.

A Projection Neural Network for Identifying Copy Number Variants

The identification of copy number variations (CNVs) helps the diagnosis of many diseases. One major hurdle in the path of CNVs discovery is that the boundaries of normal and aberrant regions cannot be distinguished from the raw data, since various types of noise contaminate them. To tackle this challenge, the total variation regularization is mostly used in the optimization problems to approximate the noise-free data from corrupted observations. The minimization using such regularization is challenging to deal with since it is non-differentiable. In this paper, we propose a projection neural network to solve the non-smooth problem. The proposed neural network has a simple one-layer structure and is theoretically assured to have the global exponential convergence to the solution of the total variation-regularized problem. The experiments on several real and simulated datasets illustrate the reasonable performance of the proposed neural network and show that its performance is comparable with those of more sophisticated algorithms.

Detection of genetic alterations in gastric cancer patients from Saudi Arabia using comparative genomic hybridization (CGH)

Background

The present study was conducted to discover genetic imbalances such as DNA copy number variations (CNVs) associated with gastric cancer (GC) and to examine their association with different genes involved in the process of gastric carcinogenesis in Saudi population.

Methods

Formalin-fixed paraffin-embedded (FFPE) tissues samples from 33 gastric cancer patients and 15 normal gastric samples were collected. Early and late stages GC samples were genotyped and CNVs were assessed by using Illumina HumanOmni1-Quad v.1.0 BeadChip.

Results

Copy number gains were more frequent than losses throughout all GC samples compared to normal tissue samples. The mean number of the altered chromosome per case was 64 for gains and 40 for losses, and the median aberration length was 679115bp for gains and 375889bp for losses. We identified 7 high copy gain, 52 gains, 14 losses, 32 homozygous losses, and 10 copy neutral LOHs (loss of heterozygosities). Copy number gains were frequently detected at 1p36.32, 1q12, 1q22, 2p11.1, 4q23-q25, 5p12-p11, 6p21.33, 9q12-q21.11, 12q11-q12, 14q32.33, 16p13.3, 17p13.1, 17q25.3, 19q13.32, and losses at 1p36.23, 1p36.32, 1p32.1, 1q44, 3q25.2, 6p22.1, 6p21.33, 8p11.22, 10q22.1, 12p11.22, 14q32.12 and 16q24.2. We also identified 2 monosomy at chromosome 14 and 22, 52 partially trisomy and 22 whole chromosome 4 neutral loss of heterozygosities at 13q14.2-q21.33, 5p15.2-p15.1, 5q11.2-q13.2, 5q33.1-q34 and 3p14.2-q13.12. Furthermore, 11 gains and 2 losses at 1p36.32 were detected for 11 different GC samples and this region has not been reported before in other populations. Statistical analysis confirms significant association of H. pylori infection with T4 stage of GC as compare to control and other stages.

Conclusions

We found that high frequency of copy number gains and losses at 1p36.23, 1p32.1, 1p36.32, 3q25.2, 6p21.33 and 16q24.2 may be common events in gastric cancer. While novel CNVs at 1p36.32 harbouring PRDM16, TP73 and TP73-AS1 genes showed 11 gains and 2 losses for 11 different GC cases and this region is not reported yet in Database of Genomic Variants may be specific to Saudi population.

Heavy-Tailed Noise Suppression and Derivative Wavelet Scalogram for Detecting DNA Copy Number Aberrations

Most existing array comparative genomic hybridization (array CGH) data processing methods and evaluation models assumed that the probability density function (pdf) of noise in array CGH data is a Gaussian distribution. However, in practice, such noise distribution is peaky and heavy-tailed. Therefore, a Gaussian pdf is not adequate to approximate the noise in array CGH data and hence introduces wrong detections of chromosomal aberrations and leads misunderstanding on disease pathogenesis. A more accurate and sufficient model of noise in array CGH data is necessary and beneficial to the detection of DNA copy number variations. We analyze the real array CGH data from different platforms and show that the distribution of noise in array CGH data is fitted very well by generalized Gaussian distribution (GGD). Based on our new noise model, we propose a novel array CGH processing method combining the advantages of both the smoothing and segmentation approaches. The new method uses generalized Gaussian bivariate shrinkage function and one-directional derivative wavelet scalogram in generalized Gaussian noise. In the smoothing step, with the new generalized Gaussian noise model, we derive the heavy-tailed noise suppression algorithm in stationary wavelet domain. In the segmentation step, the 1D Gaussian derivative wavelet scalogram is employed to detect break points. Both real and simulated array CGH data with different noises (such as Gaussian noise, GGD noise, and real noise) are used in our experiments. We demonstrate that our new method outperforms other state-of-the-art methods, in terms of both root mean squared errors and receiver operating characteristic curves.

Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics

The concept of synteny, or conservation of genes on the same chromosome, traces its origins to the early days of Drosophila genetics. This discovery emerged from comparisons of linkage maps from different species of Drosophila with the goal of understanding the process of speciation. H. J. Muller published a landmark article entitled Bearings of the "Drosophila" work on systematics, where he synthesized genetic and physical map data and proposed a model of speciation and chromosomal gene content conservation. These models have withstood the test of time with the advent of molecular genetic analysis from protein to genome level variation. Muller's ideas provide a framework to begin to answer questions about the evolutionary forces that shape the structure of the genome.

Performance comparison of two whole genome amplification techniques in frame of multifactor preimplantation genetic testing

PURPOSE

To compare multiple displacement amplification and OmniPlex whole genome amplification technique performance during array comparative genome hybridization (aCGH), Sanger sequencing, SNaPshot and fragment size analysis downstream applications in frame of multifactor embryo preimplantation genetic testing.

METHODS

Preclinical workup included linked short tandem repeat (STR) marker selection and primer design for loci of interest. It was followed by a family haplotyping, after which an in vitro fertilization preimplantation genetic testing (IVF-PGT) cycle was carried out. A total of 62 embryos were retrieved from nine couples with a confirmed single gene disorder being transmitted in their family with various inheritance traits-autosomal dominant (genes-ACTA2, HTT, KRT14), autosomal recessive (genes-ALOX12B, TPP1, GLB1) and X-linked (genes-MTM1, DMD). Whole genome amplification (WGA) for the day 5 embryo trophectoderm single biopsies was carried out by multiple displacement amplification (MDA) or polymerase chain reaction (PCR)-based technology OmniPlex and was used for direct (Sanger sequencing, fragment size analysis, SNaPshot) and indirect mutation assessment (STR marker haplotyping), and embryo aneuploidy testing by array comparative genome hybridization (aCGH).

RESULTS

Family haplotyping revealed informative/semi-informative microsatellite markers for all clinical cases for all types of inheritance. Indirect testing gave a persuasive conclusion for all embryos assessed, which was confirmed through direct testing. The overall allele dropout (ADO) rate was higher for PCR-based WGA, and MDA shows a better genomic recovery scale. Five euploid embryos were subjected to elective single embryo transfer (eSET), which resulted in four clinical pregnancies and birth of two healthy children, which proved free of disease causative variants running in the family postnataly.

CONCLUSIONS

A developed multifactor PGT protocol can be adapted and applied to virtually any genetic condition and is capable of improving single gene disorder preimplantation genetic testing in a patient-tailored manner thus increasing pregnancy rates, saving costs and increasing patient reliability.

Simultaneous involvement of 11q23 translocation resulting in chimeric MLL-AFF1 and a second translocation [t (9;21) (p13; p11.2)] in an infant acute lymphoblastic leukemia patient at relapse: A case report

RATIONALE

Three-way translocations occasionally occur in MLL-AFF1 fusion and other fusion gene. However, the complex chromosomal rearrangements in the study were the first report.

PATIENT CONCERNS

We present novel cryptic and complex chromosomal rearrangements [der (21) t (9; 21) (p13; p11.2)] in an infant patient with relapsed acute lymphoblastic leukemia (ALL).

DIAGNOSES

The diagnosis was based on morphologic, cytochemical, and immunophenotypic criteria proposed by the French-American-British Committee, and karyotype, fluorescence in situ hybridization, array comparative genomic hybridization.

INTERVENTIONS

The patient was given chemotherapy with standard protocol for ALL.

OUTCOMES

The patient had unfavorable prognostic outcome based on the cytogenetic and molecular cytogenetic markers. After short remission, the patient relapsed.

LESSONS

MLL-AFF1, resulting from t(4;11)(q21;q23), is regarded as the hallmark of infant t(4;11) pre-B/mixed B-ALL. It is associated with a dismal prognosis and the multiple-way translocation involving chromosomes 4, 11 and 11 may function as an enhancer.

Expanded Genomic Profiling of Circulating Tumor Cells in Metastatic Breast Cancer Patients to Assess Biomarker Status and Biology Over Time (CALGB 40502 and CALGB 40503, Alliance)

Purpose: We profiled circulating tumor cells (CTCs) to study the biology of blood-borne metastasis and to monitor biomarker status in metastatic breast cancer (MBC).Methods: CTCs were isolated from 105 patients with MBC using EPCAM-based immunomagnetic enrichment and fluorescence-activated cells sorting (IE/FACS), 28 of whom had serial CTC analysis (74 samples, 2-5 time points). CTCs were subjected to microfluidic-based multiplex QPCR array of 64 cancer-related genes (n = 151) and genome-wide copy-number analysis by array comparative genomic hybridization (aCGH; n = 49).Results: Combined transcriptional and genomic profiling showed that CTCs were 26% ESR1-ERBB2-, 48% ESR1+ERBB2-, and 27% ERBB2+ Serial testing showed that ERBB2 status was more stable over time compared with ESR1 and proliferation (MKI67) status. While cell-to-cell heterogeneity was observed at the single-cell level, with increasingly stable expression in larger pools, patient-specific CTC expression "fingerprints" were also observed. CTC copy-number profiles clustered into three groups based on the extent of genomic aberrations and the presence of large chromosomal imbalances. Comparative analysis showed discordance in ESR1/ER (27%) and ERBB2/HER2 (23%) status between CTCs and matched primary tumors. CTCs in 65% of the patients were considered to have low proliferation potential. Patients who harbored CTCs with high proliferation (MKI67) status had significantly reduced progression-free survival (P = 0.0011) and overall survival (P = 0.0095) compared with patients with low proliferative CTCs.Conclusions: We demonstrate an approach for complete isolation of EPCAM-positive CTCs and downstream comprehensive transcriptional/genomic characterization to examine the biology and assess breast cancer biomarkers in these cells over time. Clin Cancer Res; 24(6); 1486-99. ©2018 AACR.

Prematurity, ventricular septal defect and dysmorphisms are independent predictors of pathogenic copy number variants: a retrospective study on array-CGH results and phenotypical features of 293 children with neurodevelopmental disorders and/or multiple congenital anomalies

BACKGROUND

Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician.

METHOD

We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016. The aim of the study was to analyze clinical and molecular cytogenetic data in order to identify what elements could be useful to interpret unknown or poorly described aberrations. Comparison of phenotype and cytogenetic characteristics through univariate analysis and multivariate logistic regression was performed.

RESULTS

Copy number variations (CNVs) with a frequency < 1% were detected in 225 patients of the total sample, while 68 patients presented only variants with higher frequency (heterozygous deletions or amplification) and were considered to have negative aCGH. Proved pathogenic CNVs were detected in 70 patients (20.6%). Delayed psychomotor development, intellectual disability, intrauterine growth retardation (IUGR), prematurity, congenital heart disease, cerebral malformations and dysmorphisms correlated to reported pathogenic CNVs. Prematurity, ventricular septal defect and dysmorphisms remained significant predictors of pathogenic CNVs in the multivariate logistic model whereas abnormal EEG and limb dysmorphisms were mainly detected in the group with likely pathogenic VOUS. A flow-chart regarding the care for patients with NDD and/or MCA and/or dysmorphisms and the interpretation of aCGH has been made on the basis of the data inferred from this study and literature.

CONCLUSION

Our work contributes to make the investigative process of CNVs more informative and suggests possible directions in aCGH interpretation and phenotype correlation.

Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools

The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches. Via hybridization-mediated detection of entire genes or genetic polymorphisms in such genes and intergenic regions these so called "DNA chips" have been successfully applied for distinguishing very closely related microbial species and strains. Second and even more phenomenal, next generation sequencing (NGS) has facilitated the assessment of the complete nucleotide sequence of entire microbial genomes. This technology currently provides the most detailed level of bacterial genotyping and hence allows for the resolution of microbial spread and short-term evolution in minute detail. We will here review the very recent history of these two technologies, sketch their usefulness in the elucidation of the spread and epidemiology of mostly hospital-acquired infections and discuss future developments.

Outcomes of IVF cycles coupled with PGS by aCGH of embryos from donor and autologous oocytes, transferred after vitrification to women of advanced maternal age

It is well documented that aneuploidy rate in preimplantation embryos increases with the mother's age, and at the same time the number of oocytes diminishes. Consequently, for patients of advanced maternal age two options are available to overcome these limitations: use of oocytes from young donors, or use of own oocytes coupled with preimplantation genetic screening (PGS) for 24 chromosomes. However, it is not clear which strategy might be more effective. The aim of this retrospective study was to evaluate outcomes of IVF cycles coupled with transfer of vitrified embryos from donor or autologous oocytes, both with or without PGS. Our results demonstrate that while after PGS clinical pregnancy, twin pregnancy and spontaneous abortion rates are similar for embryos from donor and autologous oocytes, these rates are dramatically worse in all cycles without PGS. Therefore, PGS can be recommended as a screening method to all patients of advanced maternal age even when donor oocytes are used.

Imprinted NanoVelcro Microchips for Isolation and Characterization of Circulating Fetal Trophoblasts: Toward Noninvasive Prenatal Diagnostics

Circulating fetal nucleated cells (CFNCs) in maternal blood offer an ideal source of fetal genomic DNA for noninvasive prenatal diagnostics (NIPD). We developed a class of nanoVelcro microchips to effectively enrich a subcategory of CFNCs, i.e., circulating trophoblasts (cTBs) from maternal blood, which can then be isolated with single-cell resolution by a laser capture microdissection (LCM) technique for downstream genetic testing. We first established a nanoimprinting fabrication process to prepare the LCM-compatible nanoVelcro substrates. Using an optimized cTB-capture condition and an immunocytochemistry protocol, we were able to identify and isolate single cTBs (Hoechst+/CK7+/HLA-G+/CD45-, 20 μm > sizes > 12 μm) on the imprinted nanoVelcro microchips. Three cTBs were polled to ensure reproducible whole genome amplification on the cTB-derived DNA, paving the way for cTB-based array comparative genomic hybridization (aCGH) and short tandem repeats analysis. Using maternal blood samples collected from expectant mothers carrying a single fetus, the cTB-derived aCGH data were able to detect fetal genders and chromosomal aberrations, which had been confirmed by standard clinical practice. Our results support the use of nanoVelcro microchips for cTB-based noninvasive prenatal genetic testing, which holds potential for further development toward future NIPD solution.

Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders

Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe-interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders. Long-range polymerase chain reaction (PCR) is a traditional approach to obtain CNV breakpoint junction, but this method is inefficient when challenged by structural complexity such as often found at the PLP1 locus in association with Pelizaeus-Merzbacher disease (PMD). Here we introduced 'capture and single-molecule real-time sequencing' (cap-SMRT-seq) and newly developed 'asymmetry linker-mediated nested PCR walking' (ALN-walking) for CNV breakpoint sequencing in 49 subjects with PMD-associated CNVs. Remarkably, 29 (94%) of the 31 CNV breakpoint junctions unobtainable by conventional long-range PCR were resolved by cap-SMRT-seq and ALN-walking. Notably, unexpected CNV complexities, including inter-chromosomal rearrangements that cannot be resolved by aCGH, were revealed by efficient breakpoint sequencing. These sequence-based structures of PMD-associated CNVs further support the role of DNA replicative mechanisms in CNV mutagenesis, and facilitate genotype-phenotype correlation studies. Intriguingly, the lengths of gained segments by CNVs are strongly correlated with clinical severity in PMD, potentially reflecting the functional contribution of other dosage-sensitive genes besides PLP1. Our study provides new efficient experimental approaches (especially ALN-walking) for CNV breakpoint sequencing and highlights their importance in uncovering CNV mutagenesis and pathogenesis in genomic disorders.

The Molecular Revolution in Cutaneous Biology: Era of Cytogenetics and Copy Number Analysis

Development of karyotyping techniques in the 1950s sparked groundbreaking reports of chromosomal aberrations in cancer, such as the Philadelphia chromosome in chronic myelogenous leukemia in 1960, followed by a number of others. Spatial resolution of karyotyping is limited and vital tumor cells are required for metaphase preparation. To overcome these limitations, DNA hybridization techniques were developed. In situ hybridization of radioactively or fluorescence labeled RNA probes onto tumor samples allowed the identification of specific genomic regions, translocations and copy number alterations. However, it is only suited for a limited number of candidate genes or regions. Genome-wide copy number analysis was made possible by the development of comparative genomic hybridization. It compares an entire cancer genome to a normal genome by differential fluorescence labeling and hybridization onto normal metaphase chromosomes. Replacing the metaphase chromosomes with arrays of oligonucleotides significantly increased the resolution. Karyotypic analysis of melanomas could demonstrate chromosomal aberrations decades ago. However, only CGH allowed understanding the complex melanoma genomes. Based on mutation analysis and CGH data, Boris Bastian and his group changed our view of melanoma towards a variety of genetically distinct tumors. Recent next generation sequencing allows simultaneous mutation, translocation and copy number analysis, and thereby accelerates melanoma research.