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Greig cephalopolysyndactyly syndrome (GCPS) is a rare genetic disorder characterized by macrocephaly, prominent forehead, hypertelorism, preaxial and/or postaxial polydactyly, and cutaneous syndactyly. Mutations that cause haploinsufficiency in the zinc finger protein family member 3 (GLI3) gene, which is located on the short (p) arm p14 region of chromosome 7 (Chr.7), have been associated with this syndrome. Here, a case of prenatal GCPS with haploinsufficiency of the GLI3 gene is presented. A 32-year-old woman, in her 21st week of the first pregnancy, was referred to our center for cytogenetic analysis of amniotic fluid because of the detection of polyhydramnios, polydactyly, aortic stenosis, and the absence of vesica biliaris visualization on fetal ultrasound. Chromosome analysis was terminated with an interstitial short arm (p12-p15.1) deletion of chromosome 7 consisting of the GLI3 gene region (7p14). The presence of the short arm terminal region of the relevant chromosome was confirmed by fluorescence in situ hybridization analysis. Array comparative genomic hybridization technique verified the breakpoint regions and revealed a 17.4 Mb deletion covering the GLI3 gene. To date, reported prenatal cases with GCPS syndrome are very rare. Here we present a case of GCPS syndrome diagnosed in the prenatal period due to a de novo unbalanced chromosomal rearrangement. [ABSTRACT FROM AUTHOR]

Complex chromosomal rearrangements are rare events compatible with survival, consisting of an imbalance and/or position effect of one or more genes, that contribute to a range of clinical presentations. The investigation and diagnosis of these cases are often difficult. The interpretation of the pattern of pairing and segregation of these chromosomes during meiosis is important for the assessment of the risk and the type of imbalance in the offspring. Here, we investigated two unrelated pediatric carriers of complex rearrangements of chromosome 7. The first case was a 2-year-old girl with a severe phenotype. Conventional cytogenetics evidenced a duplication of part of the short arm of chromosome 7. By array-CGH analysis, we found a complex rearrangement with three discontinuous trisomy regions (7p22.1p21.3, 7p21.3, and 7p21.3p15.3). The second case was a newborn investigated for hypodevelopment and dimorphisms. The karyotype analysis promptly revealed a structurally altered chromosome 7. The array-CGH analysis identified an even more complex rearrangement consisting of a trisomic region at 7q11.23q22 and a tetrasomic region of 4.5 Mb spanning 7q21.3 to q22.1. The mother's karyotype examination revealed a complex rearrangement of chromosome 7: the 7q11.23q22 region was inserted in the short arm at 7p15.3. Finally, array-CGH analysis showed a trisomic region that corresponds to the tetrasomic region of the son. Our work proved that the integration of several technical solutions is often required to appropriately analyze complex chromosomal rearrangements in order to understand their implications and offer appropriate genetic counseling. [ABSTRACT FROM AUTHOR]

Background: Akin to cervical squamous intra-epithelial neoplasia (CIN), anal squamous intra-epithelial lesion (a-SIL) is attributed to persistent infection with high-risk human papilloma virus infection. Amplification of human telomerase reverse transcriptase (hTERT) gene and aneuploidy are known to correlate with CIN evolution. It is plausible that the underlying genetic events in a-SIL are similar. We conducted this cross-sectional analytical study with the objective of determining expression of hTERT gene expression and chromosome 7, as marker of cell ploidy in a-SIL. Methods: Conventional anal cytology was performed in 86 adult consenting subjects with history of receptive anal intercourse (RAI) and 4 controls without history of RAI. Cases with a-SIL and controls were subjected to fluorescent in-situ hybridization (FISH) to evaluate hTERT gene and chromosome 7 expression, as marker of cell ploidy. Results were expressed as number of abnormal nuclei (≥3 respective signals), maximum degree of amplification, mean signals/nucleus and proportion of cases showing abnormal nuclei. Results: Twenty cases showed a-SIL; with 15 atypical squamous cells of undetermined significance (ASCUS), 3 low grade squamous intra-epithelial lesion (LSIL) and 2 cases of high-risk cytology. Expression of both hTERT gene and chromosome 7 increased from controls to ASCUS to LSIL with concomitant increase in proportion of cases having abnormal hTERT gene and chromosome 7 expression. Conclusions: Positive association of hTERT gene with a-SIL suggests its possible role in evolution of anal squamous abnormalities. Increase in chromosome 7 also correlated positively with a-SIL. These findings corroborate the similarities between squamous carcinogenesis in CIN and a-SIL.

Background: Akin to cervical squamous intra-epithelial neoplasia (CIN), anal squamous intra-epithelial lesion (a-SIL) is attributed to persistent infection with high-risk human papilloma virus infection. Amplification of human telomerase reverse transcriptase (hTERT) gene and aneuploidy are known to correlate with CIN evolution. It is plausible that the underlying genetic events in a-SIL are similar. We conducted this cross-sectional analytical study with the objective of determining expression of hTERT gene expression and chromosome 7, as marker of cell ploidy in a-SIL. Methods: Conventional anal cytology was performed in 86 adult consenting subjects with history of receptive anal intercourse (RAI) and 4 controls without history of RAI. Cases with a-SIL and controls were subjected to fluorescent in-situ hybridization (FISH) to evaluate hTERT gene and chromosome 7 expression, as marker of cell ploidy. Results were expressed as number of abnormal nuclei (≥3 respective signals), maximum degree of amplification, mean signals/nucleus and proportion of cases showing abnormal nuclei. Results: Twenty cases showed a-SIL; with 15 atypical squamous cells of undetermined significance (ASCUS), 3 low grade squamous intra-epithelial lesion (LSIL) and 2 cases of high-risk cytology. Expression of both hTERT gene and chromosome 7 increased from controls to ASCUS to LSIL with concomitant increase in proportion of cases having abnormal hTERT gene and chromosome 7 expression. Conclusions: Positive association of hTERT gene with a-SIL suggests its possible role in evolution of anal squamous abnormalities. Increase in chromosome 7 also correlated positively with a-SIL. These findings corroborate the similarities between squamous carcinogenesis in CIN and a-SIL. [ABSTRACT FROM AUTHOR]

Abstract Background Tick-borne encephalitis (TBE) is the main tick-borne viral infection in Eurasia. Its manifestations range from inapparent infections and fevers with complete recovery to debilitating or fatal encephalitis. The basis of this heterogeneity is largely unknown, but part of this variation is likely due to host genetic. We have previously found that BALB/c mice exhibit intermediate susceptibility to the infection of TBE virus (TBEV), STS mice are highly resistant, whereas the recombinant congenic strain CcS-11, carrying 12.5% of the STS genome on the background of the BALB/c genome is even more susceptible than BALB/c. Importantly, mouse orthologs of human TBE controlling genes Oas1b, Cd209, Tlr3, Ccr5, Ifnl3 and Il10, are in CcS-11 localized on segments derived from the strain BALB/c, so they are identical in BALB/c and CcS-11. As they cannot be responsible for the phenotypic difference of the two strains, we searched for the responsible STS-derived gene-locus. Of course the STS-derived genes in CcS-11 may operate through regulating or epigenetically modifying these non-polymorphic genes of BALB/c origin. Methods To determine the location of the STS genes responsible for susceptibility of CcS-11, we analyzed survival of TBEV-infected F2 hybrids between BALB/c and CcS-11. CcS-11 carries STS-derived segments on eight chromosomes. These were genotyped in the F2 hybrid mice and their linkage with survival was tested by binary trait interval mapping. We have sequenced genomes of BALB/c and STS using next generation sequencing and performed bioinformatics analysis of the chromosomal segment exhibiting linkage with TBEV survival. Results Linkage analysis revealed a novel suggestive survival-controlling locus on chromosome 7 linked to marker D7Nds5 (44.2 Mb). Analysis of this locus for polymorphisms between BALB/c and STS that change RNA stability and genes’ functions led to detection of 9 potential candidate genes: Cd33, Klk1b22, Siglece, Klk1b16, Fut2, Grwd1, Abcc6, Otog, and Mkrn3. One of them, Cd33, carried a nonsense mutation in the STS strain. Conclusions The robust genetic system of recombinant congenic strains of mice enabled detection of a novel suggestive locus on chromosome 7. This locus contains 9 candidate genes, which will be focus of future studies not only in mice but also in humans.

Abstract Background Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP array typing. Based on these data, we discuss the UPDs and their underlying trisomy 7 formation mechanisms. Results A whole chromosome 7 maternal iUPD was confirmed in 28.8%, a mixture or complete maternal hUPD in 71.2% of patients. Conclusions We could demonstrate that nondisjunction mechanism affecting chromosome 7 are similar to that of the chromosomes more frequently involved in trisomy (and/or UPD), and that mechanisms other than trisomic rescue have a lower significance than previously suspected. Furthermore, we suggest SNP array typing for future parent- and cell-stage-of origin studies in human aneuploidies as they allow the definite classification of trisomies and UPDs, and provide information on recombinational events and their suggested association with aneuploidy formation.

Study advances with a childhood case of partial deletion of the long arm of chromosome 7. The patient is a 36-month-old girl with growth retardation, mild mental retardation and delayed bone age. She showed no signs of hypotelorism, upslanting palpebral fissures, epicanthal folds, low-set ears, or flat and broad nasal bridge. Microarray testing using the Affymetrix CytoScan HD array revealed an approximately 58 kb deletion at 7q31.1 in the girl and her father, suggesting paternal origin. As the patient had no characteristic facial features, 7q deletions had not been considered. This case broadens the range of case presentations for microdeletions of chromosome 7.

The duplication of the short arm of chromosome 7 as de novo is extremely rare. The phenotype spectrum varies depending on the region of duplication. We report a case of de novo duplication of chromosomal region 7p21.1p22.2 in a three-year-old male child with autism who presented to the Sultan Qaboos University Hospital in Muscat, Oman, in January 2012. The patient was diagnosed with craniofacial dysmorphism, global developmental delay, hypotonia and bilateral cryptorchidism. The duplication was detected by conventional G-banded karyotype analysis/fluorescence in situhybridisation and confirmed by array comparative genomic hybridisation. To the best of the authors’ knowledge, this is the first report of chromosomal region 7p21.1 involvement in an autistic patient showing features of a 7p duplication phenotype. Identifying genes in the duplicated region using molecular techniques is recommended to promote characterisation of the phenotype and associated condition. It may also reveal the possible role of these genes in autism spectrum disorder.

Chromosome 7 abnormalities in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) heralds a poor prognosis. However its prevalence, morphological characteristics and clinical impact in MDS and AML in Indian subcontinent is sparsely reported. This was an observational cross-sectional study performed to evaluate the clinico-pathological profiles of MDS/AML patients with chromosome 7 abnormalities over a period of 4 years. 724 cases of MDS (n = 150) and AML (n = 574) were evaluated. Abnormal karyotype was detected in 49% (43/88) patients of MDS and 44% (127/289) cases of AML. Chromosome 7 abnormalities were detected in 18% cases of MDS (16/88) and 6.5% (19/289) cases of AML. Sole chromosome 7 abnormalities were detected in 5.7% (5/88) and 2.7% (8/289) and in adjunct to complex abnormalities in 7.9 and 3.1% cases of MDS and AML respectively. Morphologically, dyserythropoiesis, dysmyelopoiesis and eosinophilia were seen in 100, 66 and 56% cases of MDS and 38, 40 and 21% cases of AML. Majority of the patients had an aggressive natural course and outcome was dismal. Chromosome 7 abnormalities are strongly associated with the presence of morphological dysplasia and eosinophilia, irrespective of the type of aberration. It is invariably associated with very poor outcome. [ABSTRACT FROM AUTHOR]

Absent abdominal muscles, cryptorchidism, and hydroureteronephrosis are known to occur in the prune belly syndrome (PBS). We present a male with absent abdominal muscles, severe neurologic damage, with global developmental delay, hydroureteronephrosis, and cryptorchidism. The patient also had arthrogryposis multiplex congenital, low set ears, short neck, micrognathia, bilateral total ptosis, and bilateral clubfeet. Genetic testing (CGH array) revealed 3 novel duplications of unknown clinical significance at 7q11.23, 9q22.32 (PTCH 1 gene), and 12q21.32 (CEP 290 gene). Conclusion: We feel that our patient represents a novel entity, henceforth not described in the literature.

Background: Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP array typing. Based on these data, we discuss the UPDs and their underlying trisomy 7 formation mechanisms. Results: A whole chromosome 7 maternal iUPD was confirmed in 28.8%, a mixture or complete maternal hUPD in 71.2% of patients. Conclusions: We could demonstrate that nondisjunction mechanism affecting chromosome 7 are similar to that of the chromosomes more frequently involved in trisomy (and/or UPD), and that mechanisms other than trisomic rescue have a lower significance than previously suspected. Furthermore, we suggest SNP array typing for future parent- and cell-stage-of origin studies in human aneuploidies as they allow the definite classification of trisomies and UPDs, and provide information on recombinational events and their suggested association with aneuploidy formation. [ABSTRACT FROM AUTHOR]

Introduction: To compare the efficacy of silver in situ hybridization (SISH) and immunohistochemistry (IHC) in detecting MET and IGF1R alterations and to investigate their prevalence and prognostic significance. A possible correlation between MET receptor expression, MET gene alterations and the two most frequent occurring EGFR gene mutations was also investigated. Materials and methods: Stage I to IIIA tumors from 326 patients with NSCLC were immunohistochemically tested for protein expression of MET and IGF-1. Their cytoplasmic expression was compared with the gene copy number of the MET and IGF1Rgenes by SISH in paraffin-embedded, formalin-fixed material. Correlations were made with the immunohistochemical expression of two frequent EGFR mutations and clinicopathological variables. Univariate and multivariate survival analyses was used to evaluate the prognostic efficacy of the tested markers. Results: In univariate analyses, high cytoplasmic MET expression showed a significant negative prognostic effect in adenocarcinoma patients (p = 0.026). MET gene to chromosome 7 ratio was a significant positive prognostic marker (p = 0.005), probably only due to the highly negative prognostic significance of chromosome 7 polysomy (p = 0.002). High IGF1R gene copy number was a negative prognostic marker for all NSCLC patients (p = 0.037). In the multivariate analysis, polysomy of chromosome 7 in tumor cells correlated significantly and independently with a poor prognosis (p = 0.011). In patients with adenocarcinoma, a high cytoplasmic MET expression was an independent negative prognostic marker (p = 0.013). In males a high IGF1R gene copy number to chromosome 15 count ratio was significantly and independently correlated to a poor prognosis (p = 0.018). Conclusion: MET protein expression provides superior prognostic information compared with SISH. Polysomy of chromosome 7 is an independent negative prognostic factor in NSCLC patients. This finding has an important implication while examining genes located on chromosome 7 by means of SISH. High IGF1R gene copy number to chromosome 15 count ratio is an independent predictor of inferior survival in male patients with primary NSCLC. [ABSTRACT FROM AUTHOR]

Background: Chromosome 7 aberrations in renal cell carcinoma (RCC) have been reported in papillary renal cell carcinoma (pRCC) and clear cell renal cell carcinoma (ccRCC). However, the implication of these anomalies on prognosis and survival is still unclear. RCC Chromosome 7 aberrations have commonly been detected by fluorescent in situ hybridization and chromogenic in situ hybridization but not silver in situ hybridization (SISH). Aim: The purpose was to report chromosome 7 aberrations in ccRCC and pRCC using SISH in paraffin-embedded tissues and determine the association between the anomalies with clinical and pathological features. Materials and Methods: Cases of ccRCC and pRCC from University Malaya Medical Centre (2001-2009) were analyzed. Chromosome 7 staining was performed using an automated SISH method and association tests between chromosomal anomalies, clinical features and survival were performed. Results: SISH is a feasible technique to detect chromosome 7 aberration in RCC. Chromosome 7 aberrations with nuclear grading, staging and survival yielded no significant correlation. Surprisingly, there was a significant association between gender and chromosome 7 expressions. Though grade did not reach statistical significance for survival in our RCC cases, there was a significant correlation between overall survival with race and stage. Conclusion: Chromosome 7 aberrations in ccRCC showed no prognostic significance. Nevertheless, staging and grading systems that include prognostic variables could hold better promise.

Previous results of fine mapping for quantitative trait loci affecting intramuscular fat content identified a 3.0-Mb chromosome interval on porcine chromosome 7, which contains at least 9 genes, based on the pig genome assembly. Therefore, we proposed these nine genes (LOC100154481, LOC100155711, LOC100155276, SPATA7, PTPN21, ZCH14, EML5, TTC8, and FOXN3) as positional candidate genes. The coding exons of the nine genes were characterized, and 45 polymorphisms were detected in F2 Duroc × Meishan population. Within the nine genes, 10 non-synonymous substitutions and 1 insertion were genotyped among three European breeds (Landrace, Large White, and Duroc) and 1 Chinese breed (Meishan). Genotyping data was used to perform the haplotype analysis. Polymorphisms were found in all the studied genes, except ZCH14. We surveyed the frequency of 33 haplotypes that formed non-synonymous substitutions in four breeds. One of them was distributed widely in the Landrace, Large White, and Meishan breeds, but not in Duroc. Each breed had different major haplotypes.

Objective: To present the prenatal diagnosis and molecular cytogenetic characterization of de novo partial trisomy 7p (7p15.3→pter) and partial monosomy 13q (13q33.3→qter) associated with Dandy-Walker malformation (DWM), abnormal skull development, microcephaly and multiple congenital anomalies. Materials, Methods and Results: A 42-year-old woman, gravida 6, para 1, was referred for amniocentesis at 18 weeks of gestation because of her advanced maternal age. Amniocentesis revealed an aberrant derivative chromosome 13, or der(13). The parental karyotypes were normal. Spectral karyotyping showed that the der(13) was derived from a translocation of chromosomes 7 and 13. Fluorescence in situ hybridization using subtelomeric probes revealed three signals of 7pTEL and only one signal of 13qTEL, indicating a translocation between 7p and 13q in the der(13). Array-based comparative genomic hybridization demonstrated partial trisomy 7p (7p15.3-p22.3) and partial monosomy 13q (13q33.3-q34). The karyotype was 46,XY,der(13)t(7;13)(p15.3;q33.3). Polymorphic DNA marker analysis revealed the paternal origin of the aberrant chromosome. Level II ultrasound at 24 weeks of gestation revealed microcephaly, an irregular-shaped skull, DWM, nuchal edema and transposition of the great arteries. Conclusion: Spectral karyotyping, fluorescence in situ hybridization and array-based comparative genomic hybridization are useful for prenatal investigation of the nature of a de novo aberrant derivative chromosome. Partial trisomy 7p (7p15.3→pter) and partial monosomy 13q (13q33.3→qter) can be associated with DWM, microcephaly, abnormal skull development, nuchal edema and cardiovascular defects on prenatal ultrasound.

OBJECTIVE: To develop a scoring system based on clinical findings to assist pediatricians in the diagnosis of William syndrome and to delineate when the fluorescent in-situ hybridization test to detect the microdeletion at 7q11.23 may be needed. METHODS: The fluorescent in-situ hybridization test was performed on 20 patients presenting William syndrome suggestive clinical features. Eleven studies were selected from the literature in which there were 2 groups: patients with positive or negative fluorescent in-situ hybridization tests. Forty-two clinical characteristics were compared to those reported in the literature to determine which ones were associated with the affected patients (ie, bearing deletions) using meta-analysis. The 2-tailed Fisher exact test were used so that the frequency of findings observed in fluorescent in-situ hybridization positive and fluorescent in-situ hybridization negative patients could be compared in the present study together with the patients from the literature. We developed a scoring system based on clinical findings and their significant associations with patients with positive fluorescent in-situ hybridization tests. From themean and standard-deviation values of the data from our patients, we determined the cut-off score that that indicated the need for a fluorescent in-situ hybridization test to confirm diagnosis. RESULTS: Seventeen patients were fluorescent in-situ hybridization positive, and 3 were fluorescent in-situ hybridization negative. The more discriminative findings among fluorescent in-situ hybridization positive patients were the following: typical facies, low birth weight, feeding difficulties, constipation, supravalvar aortic stenosis, mental retardation, and friendly personality. The distribution of the points among the 20 patients ranged from 19 to 28 points with a mean value of 23.3 out of a possible total of 31 points. The cut-off score that indicated the need for a fluorescent in-situ hybridization test was 20. CONCLUSIONS: Our scoring system enables physicians to differentiate between those individuals who can be reliably diagnosed as having Williams syndrome solely from the clinical findings and those who need to undergo fluorescent in-situ hybridization testing for a correct diagnosis.OBJETIVOS: Desenvolver um sistema de pontuação (Score) baseado nos achados clínicos para auxiliar os pediatras no diagnóstico clínico da Síndrome de Williams-Beuren e na indicação do teste de hibridização in situ por fluorescência para detectar a microdeleção em 7q11.23. MÉTODOS: O teste de hibridização in situ por fluorescência foi feito em 20 acometidos pela Síndrome de Williams-Beuren, nos quais 42 achados clínicos foram estudados. Para estabelecer quais desses achados estariam associados ao teste de hibridização in situ por fluorescência positivo, realizou-se uma metanálise com 11 trabalhos da literatura em que havia dois grupos, hibridização in situ por fluorescência positivo e negativo. As freqüências dos achados presentes nos indivíduos fluorescência positivo e fluorescência negativo neste estudo foram comparadas em conjunto com os pacientes da literatura através do teste exato de Fisher. Elaboramos um sistema de pontuação (score) baseado nos achados que mostraram correlação significante (p

Background: Analphoid supernumerary marker chromosomes (aSMC) constitute one of the smallest groups of SMC, and are characterized by a centromeric constriction but no detectable alpha-satellite DNA. These marker chromosomes cannot be properly identified by conventional banding techniques alone, and molecular cytogenetic methods are necessary for a detailed characterization. Analphoid SMC derived from chromosome 7 are extremely rare, with only five cases reported so far. Case presentation: In this work we report an aSMC involving the terminal long arm of chromosome 7 in a 10-year-old boy with multiple dysmorphic features and severe development delay. Cytogenetic analysis revealed a mosaic karyotype with the presence of an extra SMC, de novo, in 20% of lymphocytes and 73% of fibroblast cells. Next, we performed FISH analysis with multiple DNA probes and cCGH analysis. This identified the origin of the SMC as an analphoid marker resulting of invdup rearrangement of 7q35-qter region. Affimetrix CytoScan HD array analysis redefined the aSMC as a 15.42 Mb gain at 7q35-q36.3 (minimum tetraplicated region-chr7: 143,594,973-159,119,707; GRCh37/hg19) of maternal origin that encloses 67 OMIM genes, 16 of which associated to disease. Uniparental disomy of chromosome 7 (UPD 7) has been excluded. Conclusions: We report the first patient with an aSMC(7) derived from the terminal 7q region who has been molecularly and clinically full characterized. The use of SNParray in the characterization of SMC reveals to be a powerful tool, giving information not only about copy number variation but also about loss-of-heterozygosity and parental origin. We conclude that an integrated genome-wide copy number variation analysis, if possible associated to FISH and gene expression studies, could facilitate in the future the difficult task of establishing accurate genotype-phenotype correlations and help to improve genetic counselling. [ABSTRACT FROM AUTHOR]

Recent investigations revealed genetic analysis provides important information in management of gliomas, and we previously reported grade II- III gliomas could be classified into clinically relevant subgroups based on the DNA copy number aberrations ( CNAs). To develop more precise genetic subgrouping, we investigated the correlation between CNAs and mutational status of the gene encoding isocitrate dehydrogenase ( IDH) of those tumors. We analyzed the IDH status and CNAs of 174 adult supratentorial gliomas of astrocytic or oligodendroglial origin by PCR-based direct sequencing and comparative genomic hybridization, respectively. We analyzed the relationship between genetic subclassification and clinical features. We found the most frequent aberrations in IDH mutant tumors were the combined whole arm-loss of 1p and 19q (1p/19q codeletion) followed by gain on chromosome arm 7q (+7q). The gain of whole chromosome 7 (+7) and loss of 10q (−10q) were detected in IDH wild-type tumors. Kaplan-Meier estimates for progression-free survival showed that the tumors with mutant IDH, −1p/19q, or +7q (in the absence of +7p) survived longer than tumors with wild-type IDH, +7, or −10q. As tumors with +7 ( IDH wild-type) showed a more aggressive clinical nature, they are probably not a subtype that developed from the slowly progressive tumors with +7q ( IDH mutant). Thus, tumors with a gain on chromosome 7 (mostly astrocytic) comprise multiple lineages, and such differences in their biological nature should be taken into consideration during their clinical management. [ABSTRACT FROM AUTHOR]

Next generation sequencing methodologies are facilitating the rapid characterisation of novel structural variants at nucleotide resolution. These approaches are particularly applicable to variants initially identified using alternative molecular methods. We report a child born with bilateral postaxial syndactyly of the feet and bilateral fifth finger clinodactyly. This was presumed to be an autosomal recessive syndrome, due to the family history of consanguinity. Karyotype analysis revealed a homozygous pericentric inversion of chromosome 7 (46,XX,inv(7)(p15q21)x2) which was confirmed to be heterozygous in both unaffected parents. Since the resolution of the karyotype was insufficient to identify any putatively causative gene, we undertook medium-coverage whole genome sequencing using paired-end reads, in order to elucidate the molecular breakpoints. In a two-step analysis, we first narrowed down the region by identifying discordant read-pairs, and then determined the precise molecular breakpoint by analysing the mapping locations of “soft-clipped” breakpoint-spanning reads. PCR and Sanger sequencing confirmed the identified breakpoints, both of which were located in intergenic regions. Significantly, the 7p15 breakpoint was located 523 kb upstream of HOXA13, the locus for hand-foot-genital syndrome. By inference from studies of HOXA locus control in the mouse, we suggest that the inversion has delocalised a HOXA13 enhancer to produce the phenotype observed in our patient. This study demonstrates how modern genetic diagnostic approach can characterise structural variants at nucleotide resolution and provide potential insights into functional regulation. [ABSTRACT FROM AUTHOR]

Serum triglyceride (TG) levels are increased in extremely obese individuals, indicating abnormalities in lipid metabolism and insulin resistance. We carried out a genome scan for serum TG in 320 nuclear families segregating extreme obesity and normal weight. Three hundred eighty-two Marshfield microsatellite markers (Screening Set 11) were genotyped. Quantitative linkage analyses were performed using family regression and variance components methods. We found linkage on the 7q36 region [D7S3058, 174 centimorgan (cM), Logarithm of Odds (LOD) = 2.98] for log-transformed TG. We also found suggestive linkages on chromosomes 20 (D20S164, 101 cM, LOD = 2.34), 13 (111 cM, LOD = 2.00), and 9 (104 cM, LOD = 1.90) as well as some weaker trends for chromosomes 1, 3, 5, 10, 12, and 22. In 58 African American families, LOD scores of 3.66 and 2.62 were observed on two loci on chromosome 16: D16S3369 (64 cM) and MFD466 (100 cM).To verify the 7q36 linkage, we added 60 nuclear families, and the LOD score increased to 3.52 (empirical P < 0.002) on marker D7S3058.

Study advances with a childhood case of partial deletion of the long arm of chromosome 7. The patient is a 36-month-old girl with growth retardation, mild mental retardation and delayed bone age. She showed no signs of hypotelorism, upslanting palpebral fissures, epicanthal folds, low-set ears, or flat and broad nasal bridge. Microarray testing using the Affymetrix CytoScan HD array revealed an approximately 58 kb deletion at 7q31.1 in the girl and her father, suggesting paternal origin. As the patient had no characteristic facial features, 7q deletions had not been considered. This case broadens the range of case presentations for microdeletions of chromosome 7. [ABSTRACT FROM AUTHOR]

Receptor tyrosine kinases such as the epidermal growth factor receptor (EGFR) play an important role in a variety of malignant neoplasias, making the search for aberrations in the relevant chromosomes an important issue. Differential expression of the EGFR gene was investigated by reverse transcriptase (RT)-PCR on tissue samples of normal skin, nevi, primary melanomas, and melanoma metastases. The EGFR gene is located on chromosome 7p12.3-p12.1. To determine the number of chromosomes 7 in cell nuclei of the mentioned tissue samples we performed fluorescence in situ hybridization (FISH) on touch preparations, using a DNA probe that hybridizes specifically to the centromeric region of chromosome 7. Additionally, chromosome 7 number in interphase nuclei was determined in short-term primary cell cultures of nevi, primary melanomas, and metastases. The highest EGFR gene expression frequency was found in melanoma metastases. By FISH we detected the highest fraction of cell nuclei with more than two chromosomes 7 in the group of metastases. Our results suggest that overexpression of the EGFR gene might play an important role in metastasis of malignant melanoma. This is well reflected by polysomy 7, possibly accounting for an increased EGFRgene copy number.

The duplication of the short arm of chromosome 7 as de novo is extremely rare. The phenotype spectrum varies depending on the region of duplication. We report a case of de novo duplication of chromosomal region 7p21.1p22.2 in a three-year-old male child with autism who presented to the Sultan Qaboos University Hospital in Muscat, Oman, in January 2012. The patient was diagnosed with craniofacial dysmorphism, global developmental delay, hypotonia and bilateral cryptorchidism. The duplication was detected by conventional G-banded karyotype analysis/fluorescence in situ hybridisation and confirmed by array comparative genomic hybridisation. To the best of the authors' knowledge, this is the first report of chromosomal region 7p21.1 involvement in an autistic patient showing features of a 7p duplication phenotype. Identifying genes in the duplicated region using molecular techniques is recommended to promote characterisation of the phenotype and associated condition. It may also reveal the possible role of these genes in autism spectrum disorder. [ABSTRACT FROM AUTHOR]

7q terminal deletion syndrome is due to a loss of the distal portion of the long arm of chromosome 7; it is variable and depends on the size of the compromised region. Its clinical spectrum is wide and includes several anatomic systems. Case report: the patient is an eightyear- old girl who shows neurodevelopmental delay, absence of speech, cupped ears with overfolding helix, retrognathia, prominent incisors with gingival hyperplasia, dental malocclusion, umbilical hernia and clubfoot. The G-banding karyotype (25 metafases analyzed, 550-600 bands) reported: 46, xx, del (7) (q35), 46, xx, del (7) (pter → q35:). Phenotypic alterations differ due to chromosomal breakpoints. we compare clinical findings of the patient with case reports published in the worldwide literature. It is important to establish a clinical characterization and to perform molecular and cytogenetic studies in order to have a well-timed diagnosis and prescribe preventive management and genetic counseling. [ABSTRACT FROM AUTHOR]

Elevated heart rate (HR) is a risk factor for cardiovascular diseases. The goal of the study was to map HR trait in mice using quantitative trait locus (QTL) analysis followed by genome-wide association (GWA) analysis. The first approach provides mapping power and the second increases genome resolution. QTL analyses were performed in a C3HeB×SJL backcross. HR and systolic blood pressure (SBP) were measured by the tail-cuff plethysmography. HR was ~80 beats/min higher in SJL compared with C3HeB. There was a wide distribution of the HR (536-763 beats/min) in N2 mice. We discovered a highly significant QTL (logarithm of odds = 6.7, P < 0.001) on chromosome 7 (41 cM) for HR in the C3HeB×SJL backcross. In the Hybrid Mouse Diversity Panel (58 strains, n < 5-6/strain) we found that HR (beats/min) ranged from 546 ± 12 in C58/J to 717 ± 7 in MA/MyJ mice. SBP (mmHg) ranged from 99 ± 6 in strain I/LnJ to 151 ± 4 in strain BXA4/PgnJ. GWA analyses were done using the HMDP, which revealed a locus (64.2- 65.1 Mb) on chromosome 7 that colocalized with the QTL for elevated HR found in the C3HeBSJL backcross. The peak association was observed for 17 SNPs that are localized within three GABAA receptor genes. In summary, we used a combined genetic approach to fine map a novel elevated HR locus on mouse chromosome 7. [ABSTRACT FROM AUTHOR]

Abstract: The first step towards effective therapy of cancer is to reveal molecular profiles of all cell clones propelling tumor growth. The specific aim of this project was to develop a technology helping us to isolate patient''s single, living cells based upon their cancer-specific, cell surface biomarkers, to reveal their molecular profiles, and to isolate, from these selected cells, intact chromosomes for in situ hybridization (FISH) and for next generation sequencing (NGS). We attained this aim, while probing the cells from the ovarian cancer patients. Ovarian cancer is the most deadly of all gynecological cancers. In most of the patients with the advanced stages of this cancer, the gene for epidermal growth factors receptor (EGFR) is mutated, as the deletion variant III, resulting in the truncated transcripts and products. From these patients, we collected cells from peritoneal fluid, blood, lymph, and biopsies. We genetically engineered fluorescent and superparamagnetic single chain variable fragments (scFvs) targeting EGFRwt and EGFRvIII. Using these scFvs, we isolated single, living ovarian cancer cells and analyzed their transcripts and products. We further genetically engineered scFv targeting dsDNA. Using these scFvs, we isolated the entire single, intact chromosomes from the selected, single ovarian cancer cells for NGS and for liquid phase FISH. This novel work-flow opens new routes not only for molecular profiling of the entire spectrum of cancer cell clones in the diagnosed patient, one cell clone at a time, but also for manufacturing targeted contrast for in vivo imaging and for designing and guiding targeted delivery of therapeutic genes in cancer therapy. [Copyright &y& Elsevier]

BACKGROUND Although assisted reproductive technology (ART) is reported to result in abnormal genomic imprinting and/or altered genomic methylation, few if any studies have used high-throughput methods to analyze genomic methylation in ART embryos. We hypothesized that a microarray-based assessment of genomic methylation could be used to reveal differences between ART and normal preimplantation embryos. METHODS In this pilot study, we performed methylation-sensitive amplification of genomic DNA from preimplantation mouse blastocysts, obtained by natural mating and either maintained in vivo until E3.5 (n= 4) or cultured in vitro (n= 4) from E0.5 until E3.5. An oligonucleotide microarray was then used to perform comparative hybridization of amplified DNA, allowing us to assess relative methylation at ∼16 000 loci on mouse chromosome 7. RESULTS We show that for in vivo derived embryos, the methylation/microarray results were strikingly consistent. In contrast, all four in vitro cultured embryos showed evidence of generalized hypermethylation as well as greater locus-to-locus variability, when compared with in vivo derived embryos. Genomic segments that overlapped exons and CpG islands were most likely to be hypomethylated in both normal and experimental blastocysts. Other sequence features, such as repetitive elements, were not associated with the presence of or the degree of methylation. CONCLUSIONS We conclude that a general assessment of genomic methylation in blastocyst stage embryos is technically feasible. Data from this small sample suggest that in vitro embryo culture is associated with generalized hypermethylation as well as increased locus-to-locus variability in methylation. However, it is premature to conclude that this is a general property of in vitro cultured blastocysts. [ABSTRACT FROM AUTHOR]

Summary The genome of bread wheat ( Triticum aestivum) is predicted to be greater than 16 Gbp in size and consist predominantly of repetitive elements, making the sequencing and assembly of this genome a major challenge. We have reduced genome sequence complexity by isolating chromosome arm 7DS and applied second-generation technology and appropriate algorithmic analysis to sequence and assemble low copy and genic regions of this chromosome arm. The assembly represents approximately 40% of the chromosome arm and all known 7DS genes. Comparison of the 7DS assembly with the sequenced genomes of rice ( Oryza sativa) and Brachypodium distachyon identified large regions of conservation. The syntenic relationship between wheat, B. distachyon and O. sativa, along with available genetic mapping data, has been used to produce an annotated draft 7DS syntenic build, which is publicly available at . Our results suggest that the sequencing of isolated chromosome arms can provide valuable information of the gene content of wheat and is a step towards whole-genome sequencing and variation discovery in this important crop. [ABSTRACT FROM AUTHOR]

Abstract: Carriers of paracentric inversions (PAIs) are usually asymptomatic. However, such inversions may lead to the formation of recombinant gametes and then to an abnormal gestation. Here we report a girl with a 7q31.32 → q33 deletion secondary to a maternal PAI of chromosome 7. This finding was confirmed through FISH and whole-genome array-CGH analyses. The deficiency of the chromosome 7 observed in our patient was never described before and we did not find any known gene localized within the deficient segment that could be related to her findings of hypoplastic iliac bones, hypoplastic labia minora and postaxial polydactyly. This case highlights the fact that rare viable recombinants can be developed from PAIs, an issue that must be discussed in the genetic counseling. [Copyright &y& Elsevier]

Autism spectrum disorders are a group of highly heritable neurodevelopmental disorders with a complex genetic etiology. The International Molecular Genetic Study of Autism Consortium previously identified linkage loci on chromosomes 7 and 2, termed AUTS1 and AUTS5, respectively. In this study, we performed a high-density association analysis in AUTS1 and AUTS5, testing more than 3000 single nucleotide polymorphisms (SNPs) in all known genes in each region, as well as SNPs in non-genic highly conserved sequences. SNP genotype data were also used to investigate copy number variation within these regions. The study sample consisted of 127 and 126 families, showing linkage to the AUTS1 and AUTS5 regions, respectively, and 188 gender-matched controls. Further investigation of the strongest association results was conducted in an independent European family sample containing 390 affected individuals. Association and copy number variant analysis highlighted several genes that warrant further investigation, including IMMP2L and DOCK4 on chromosome 7. Evidence for the involvement of DOCK4 in autism susceptibility was supported by independent replication of association at rs2217262 and the finding of a deletion segregating in a sib-pair family. [ABSTRACT FROM AUTHOR]

The article presents a study which examined the association between the variation in the DNA sequence of the aquaporin-1 (AQP1) gene towards the performance of Hispanic marathon runners. The study utilized a case-control method. It revealed significant relationship between the DNA sequence variant in the AQP1 gene towards the performance of Hispanic runners.

We performed a high-density, single nucleotide polymorphism (SNP), genome-wide scan on a six-generation pedigree from Utah with seven affected males, diagnosed with autism spectrum disorder. Using a two-stage linkage design, we first performed a nonparametric analysis on the entire genome using a 10K SNP chip to identify potential regions of interest. To confirm potentially interesting regions, we eliminated SNPs in high linkage disequilibrium (LD) using a principal components analysis (PCA) method and repeated the linkage results. Three regions met genome-wide significance criteria after controlling for LD: 3q13.2–q13.31 (nonparametric linkage (NPL), 5.58), 3q26.31–q27.3 (NPL, 4.85) and 20q11.21–q13.12 (NPL, 5.56). Two regions met suggestive criteria for significance 7p14.1–p11.22 (NPL, 3.18) and 9p24.3 (NPL, 3.44). All five chromosomal regions are consistent with other published findings. Haplotype sharing results showed that five of the affected subjects shared more than a single chromosomal region of interest with other affected subjects. Although no common autism susceptibility genes were found for all seven autism cases, these results suggest that multiple genetic loci within these regions may contribute to the autism phenotype in this family, and further follow-up of these chromosomal regions is warranted.Molecular Psychiatry (2009) 14, 590–600; doi:10.1038/mp.2008.14; published online 19 February 2008 [ABSTRACT FROM AUTHOR]

Tuberculosis remains a significant global health problem: one-third of the human population is infected with Mycobacterium tuberculosis (MTB) and 10% of those are at lifetime risk of developing tuberculosis. In the majority of individuals infected, genetic determinants of susceptibility remain largely unknown due to complex multigenic control and the influence of genes—environment interactions. Genetic variation of host resistance to MTB in animal models reflects heterogeneity among humans. Stepwise dissection of these interactions will permit the deciphering of MTB's complex virulence strategy. Previously, we have characterized a mouse supersusceptibility locus (sst1) controlling antituberculosis immunity. In this study, eight host resistance quantitative trait loci (QTLs) were mapped that counter-balance the devastating effect of sst1, among which a QTL on chromosome 7 (Chr7) was most prominent. The Chr7 and sst1 loci independently control distinct resistance mechanisms to MTB, but their effects apparently converge on macrophages in remarkable synergy. Combining these resistance alleles on a C3HeB/FeJ-susceptible background reduced the lung pathology and improved survival after MTB challenge accounting for half of the difference between susceptible and resistant parental strains. These data reveal novel gene interactions controlling MTB resistance and will enable the identification of resistance gene(s) encoded within Chr7 locus.Genes and Immunity (2009) 10, 37–46; doi:10.1038/gene.2008.68; published online 11 September 2008 [ABSTRACT FROM AUTHOR]

Lung cancer accounts for over a quarter of cancer deaths, with non-small cell lung cancer (NSCLC) accounting for approximately 80% of cases. Several genome studies have been undertaken in both cell models of NSCLC and clinical samples to identify alterations underlying disease behaviour, and many have identified recurring aberrations of chromosome 7. The presence of recurring chromosome 7 alterations that do not span the well-studied oncogenes EGFR (at 7p11.2) and MET (at 7q31.2) has raised the hypothesis of additional genes on this chromosome that contribute to tumourigenesis. In this study, we demonstrated that multiple loci on chromosome 7 are indeed amplified in NSCLC, and through integrative analysis of gene dosage alterations and parallel gene expression changes, we identified new lung cancer oncogene candidates, including FTSJ2, NUDT1, TAF6, and POLR2J. Activation of these key genes was confirmed in panels of clinical lung tumour tissue as compared with matched normal lung tissue. The detection of gene activation in multiple cohorts of samples strongly supports the presence of key genes involved in lung cancer that are distinct from the EGFR and MET loci on chromosome 7. Le cancer du poumon compte pour le quart des décès dus au cancer et les cancer du poumon à grandes cellules (NSCLC pour « non-small cell lung cancer ») comptent pour environ 80% de ces cas. Plusieurs études génomiques ont été entreprises tant chez des systèmes cellulaires modèles du NSCLC que chez des échantillons cliniques pour identifier les altérations derrière le comportement pathologique. Plusieurs de ces études ont identifié des aberrations récurrentes sur le chromosome 7. La présence d’altérations récurrentes sur le chromosome 7 qui ne chevauchent pas les oncogènes largement étudiés EGFR (à 7p11.2) et MET (à 7q31.2) soulève l’hypothèse que d’autres gènes sur ce chromosome contribueraient à la tumorigénèse. Dans ce travail, les auteurs montrent que de multiples locus sur le chromosome 7 sont effectivement amplifiés chez les NSCLC. Par analyse intégrative des altérations dans le dosage génique et, parallèlement, des changements observés dans l’expression génique, les auteurs ont identifié de nouveaux oncogènes candidats pour le cancer du poumon dont FTSJ2, NUDT1, TAF6 et POLR2J. L’activation de ces gènes clés a été confirmée chez un panel de tissus pulmonaires tumoraux comparés à des tissus pulmonaires normaux correspondants. L’observation d’une activation génique chez de multiples cohortes d’échantillons supporte fortement l’existence de gènes clés impliqués dans le cancer du poumon autres que les loci EGFR et MET sur le chromosome 7. [ABSTRACT FROM AUTHOR]

Abstract: About 20% of cases with 7q deletion syndrome is associated with holoprosencephaly (HPE), due to deletion of the Sonic Hedgehog (SHH) gene (mapping to 7q36). The occurrence of severe forms of holoprosencephaly is higher in cases of 7q deletion associated with partial trisomies involving different parts of the genomes than in patients with pure 7q deletion. All cases of 7q deletion associated with 3p duplication reported to date have been associated with severe forms of holoprosencephaly, and a gene(s) on distal 3p has (have) been hypothesized to be responsible for HPE phenotype when in triple dose. Here we describe a patient with unbalanced 3p;7q translocation, showing 7q deletion (including SHH gene) and 3p duplication (complete karyotype was 46,XY,der(7)t(3;7)(p26.3;q36.1)), presenting with a relatively mild phenotype, consisting of microphthalmia and microcephaly, without cerebral anomalies typical of holoprosencephaly. Possible involvement of some genes on 3p in determining such a mild phenotype is discussed. [Copyright &y& Elsevier]

We performed a genome-wide linkage scan using highly polymorphic microsatellite markers. To minimize genetic heterogeneity, we focused on sibpairs meeting the strict diagnosis of autism. In our primary analyses, we observed a strong linkage signal (P=0.0006, 133.16 cM) on chromosome 7q at a location coincident with other linkage studies. When a more relaxed diagnostic criteria was used, linkage evidence at this location was weaker (P=0.01). The sample was stratified into families with only male affected subjects (MO) and families with at least one female affected subject (FC). The strongest signal unique to the MO group was on chromosome 11 (P=0.0009, 83.82 cM), and for the FC group on chromosome 4 (P=0.002, 111.41 cM). We also divided the sample into regression positive and regression negative families. The regression-positive group showed modest linkage signals on chromosomes 10 (P=0.003, 0 cM) and 14 (P=0.005, 104.2 cM). More significant peaks were seen in the regression negative group on chromosomes 3 (P=0.0002, 140.06 cM) and 4 (P=0.0005, 111.41 cM). Finally, we used language acquisition data as a quantitative trait in our linkage analysis and observed a chromosome 9 signal (149.01 cM) of P=0.00006 and an empirical P-value of 0.0008 at the same location. Our work provides strong conformation for an autism locus on 7q and suggestive evidence for several other chromosomal locations. Diagnostic specificity and detailed analysis of the autism phenotype is critical for identifying autism loci.Molecular Psychiatry (2006) 11, 1049–1060. doi:10.1038/sj.mp.4001874; published online 1 August 2006 [ABSTRACT FROM AUTHOR]

Uterine fibroids are some of the most common tumours of females, but relatively little is known about their molecular basis. Several studies have suggested that deletions on chromosome 7q could have a role in fibroid formation. We analysed 165 sporadic uterine fibroids to define a small 3.2 megabase (Mb) commonly deleted region on 7q22.3–q31.1, flanked by clones AC005070 and AC007567. We also used oligonucleotide microarrays to compare the expression profiles of 10 samples of normal myometrium and 15 fibroids, nine of which displayed 7q-deletions. Activating transcription factor 3, patched homolog (Drosophila), homeo box A5, death-associated protein kinase 1, and retinoic acid receptor responder 3 were downregulated, and excision repair crosscomplementing 3, transcription factor AP-2 gamma and protein kinase C beta 1 were upregulated in fibroids. New pathways were discovered related to fibroid formation. The presence or absence of 7q-deletions did not dramatically affect the global expression pattern of the tumours; changes, however, were observed in genes related to vesicular transport and nucleic acid binding.Oncogene (2005) 24, 6545–6554. doi:10.1038/sj.onc.1208784; published online 6 June 2005 [ABSTRACT FROM AUTHOR]

Prenatal trisomy 7 is usually a cell culture artifact in amniocytes with normal diploid karyotype at birth and normal fetal outcome. In the same way, true prenatal trisomy 7 mosaicism usually results in a normal child except when trisomic cells persist after birth or when trisomy rescue leads to maternal uniparental disomy, which is responsible for 5.5–7% of patients with Silver–Russell syndrome (SRS). We report here on the unusual association of SRS and Hirschsprung's disease (HSCR) in a patient with maternal uniparental heterodisomy 7 and trisomy 7 mosaicism in intestine and skin fibroblasts. HSCR may be fortuitous given its frequency, multifactorial inheritance and genetic heterogeneity. However, the presence of the trisomy 7 mosaicism in intestine as well as in skin fibroblasts suggests that SRS and HSCR might possibly be related. Such an association might result from either an increased dosage of a nonimprinted gene due to trisomy 7 mosaicism in skin fibroblasts (leading to SRS) and in intestine (leading to HSCR), or from an overexpression, through genomic imprinting, of maternally expressed imprinted allele(s) in skin fibroblasts and intestine or from a combination of trisomy 7 mosaicism and genomic imprinting. This report suggests that the SRS phenotype observed in maternal uniparental disomy 7 (mUPD(7)) patients might also result from an undetected low level of trisomy 7 mosaicism. In order to validate this hypothesis, we propose to perform a conventional and molecular cytogenetic analysis in different tissues every time mUPD(7) is displayed.European Journal of Human Genetics (2005) 13, 1013–1018. doi:10.1038/sj.ejhg.5201442; published online 25 May 2005 [ABSTRACT FROM AUTHOR]