Unbalanced Chromosomal Abnormalities Research Articles

Prenatal diagnosis of a 12q22q23.2 interstitial deletion by array CGH in a malformed fetus

We report the prenatal diagnosis of a 12q22q23.2 de novo interstitial deletion performed by array based comparative genomic hybridization (array CGH) in a fetus with cystic hygroma colli, intrauterine growth retardation, microcephaly and micrognathism.Haploinsufficiency for insuline-like growth factor 1 gene (IGF1), which is mapped in the deleted region, is suggested because of its implication in prenatal and postnatal growth and in neuronal maturation.This case demonstrates the contribution of array CGH in prenatal diagnosis for detecting small unbalanced chromosomal abnormalities in malformed fetuses and, subsequently, for genetic counselling.

Rare chromosome abnormalities, prevalence and prenatal diagnosis rates from population-based congenital anomaly registers in Europe

The aim of this study is to quantify the prevalence and types of rare chromosome abnormalities (RCAs) in Europe for 2000–2006 inclusive, and to describe prenatal diagnosis rates and pregnancy outcome. Data held by the European Surveillance of Congenital Anomalies database were analysed on all the cases from 16 population-based registries in 11 European countries diagnosed prenatally or before 1 year of age, and delivered between 2000 and 2006. Cases were all unbalanced chromosome abnormalities and included live births, fetal deaths from 20 weeks gestation and terminations of pregnancy for fetal anomaly. There were 10 323 cases with a chromosome abnormality, giving a total birth prevalence rate of 43.8/10 000 births. Of these, 7335 cases had trisomy 21,18 or 13, giving individual prevalence rates of 23.0, 5.9 and 2.3/10 000 births, respectively (53, 13 and 5% of all reported chromosome errors, respectively). In all, 473 cases (5%) had a sex chromosome trisomy, and 778 (8%) had 45,X, giving prevalence rates of 2.0 and 3.3/10 000 births, respectively. There were 1 737 RCA cases (17%), giving a prevalence of 7.4/10 000 births. These included triploidy, other trisomies, marker chromosomes, unbalanced translocations, deletions and duplications. There was a wide variation between the registers in both the overall prenatal diagnosis rate of RCA, an average of 65% (range 5–92%) and the prevalence of RCA (range 2.4–12.9/10 000 births). In all, 49% were liveborn. The data provide the prevalence of families currently requiring specialised genetic counselling services in the perinatal period for these conditions and, for some, long-term care.

Genomic SNP array as a gold standard for prenatal diagnosis of foetal ultrasound abnormalities

BackgroundWe have investigated whether replacing conventional karyotyping by SNP array analysis in cases of foetal ultrasound abnormalities would increase the diagnostic yield and speed of prenatal diagnosis in clinical practice.Findings/resultsFrom May 2009 till June 2011 we performed HumanCytoSNP-12 array (HCS) (http://www.Illumina.com) analysis in 207 cases of foetal structural abnormalities. HCS allows detecting unbalanced genomic abnormalities with a resolution of about 150/200 kb. All cases were selected by a clinical geneticist after excluding the most common aneuploidies by RAD (rapid aneuploidy detection). Pre-test genetic counselling was offered in all cases.In 24/207 (11,6%) foetuses a clinically relevant genetic abnormality was detected. Only 8/24 abnormalities would have been detected if only routine karyotyping was performed. Submicroscopic abnormalities were found in 16/207 (7,7%) cases. The array results were achieved within 1-2 weeks after amniocentesis.ConclusionsPrenatal SNP array testing is faster than karyotyping and allows detecting much smaller aberrations (~0.15 Mb) in addition to the microscopic unbalanced chromosome abnormalities detectable with karyotyping (~ > 5 Mb). Since karyotyping would have missed 66% (16/24) of genomic abnormalities in our cohort, we propose to perform genomic high resolution array testing assisted by pre-test counselling as a primary prenatal diagnostic test in cases of foetal ultrasound abnormalities.

New cytogenetically visible copy number variant in region 8q21.2

BackgroundCytogenetically visible unbalanced chromosomal abnormalities (UBCA), reported for >50 euchromatic regions of almost all human autosomes, are comprised of a few megabases of DNA, and carriers are in many cases clinically healthy. It may be speculated, that some of the UBCA may be similar or identical to copy number variants (CNV) of the human genome.ResultsHere we report on a yet unreported cytogenetically visible copy number variant (CNV) in the long arm of chromosome 8, region 8q21.2, detected in three unrelated clinically healthy carriers.ConclusionThe first description of a cytogenetically visible CNV/UBCA in 8q21.2 shows that banding cytogenetics is far from being outdated. It is a cost efficient, up-to-date method for a single cell specific overview on the whole genome, still prepared to deliver unexpected findings.

The identification of CNVs in patients and their association with diseases and phenotypes

The DNA copy number of a region of a genome is the number of copies of genomic DNA. In humans the normal copy number is two for majority of autosomes. However, discoveries have revealed that many segments of DNA, ranging in size from kilobases to megabases, can vary in copy-number. These DNA copy number variations (CNVs) are common in normal individual and contribute to our uniqueness. These changes can also influence the susceptibility to disease. Many genetic diseases that occur in families result from copy number variations. Here we report on the phenotypic and genotypic delineation of de novo CNVs in a number of cases with genetic disorders. Case 1: A 20-year-old male with severe intellectual disability and Marfanoid habitus, cleft palate, facial dysmorphism, microphthalmia and hypermetropia. Cytogenetic investigation showed an unbalanced chromosomal abnormality with an additional un-identified chromosome piece attached to the short arm of chromosome 14. A duplication of the terminal piece of the long arm of chromosome 10 (30.1 Mb) was found. Case 2: A 9-year-old female with global developmental and speech delay associated with dysmorphic features that includes longitudinal face with prominent forehead, high arched palate, and hypertelorism and alternating isotropia. Prominent fetal pads and bridged simian crease are noted in both hands. Her MRI showed diffuse brain atrophy. A duplication of a segment on the long arm of chromosome 15 as well as a deletion of the terminal part of the short arm of chromosome 8 were detected. Case 3: A 13-year-old male with mild to moderate mental retardation, obesity, and dysmorphic features that includes but not limited to micropenis, flat occiput, protruding maxilla, and hirsutism. CT scan showed moderate cerebral atrophy. Cytogenetic investigation revealed a 46 XY r(13) p11.2q32. A 20.5 Mb segment deletion on the terminal part of the long arm of chromosome 13 was found. The cases included demonstrate that CNVs play a role in genetic disorders, birth defects and patterns of malformations. The delineation of the duplicated or deleted material may help in the identification of genes that play a role in developmental processes.

Disorders caused by chromosome abnormalities

Many human genetic disorders result from unbalanced chromosome abnormalities, in which there is a net gain or loss of genetic material. Such imbalances often disrupt large numbers of dosage-sensitive, developmentally important genes and result in specific and complex phenotypes. Alternately, some chromosomal syndromes may be caused by a deletion or duplication of a single gene with pleiotropic effects. Traditionally, chromosome abnormalities were identified by visual inspection of the chromosomes under a microscope. The use of molecular cytogenetic technologies, such as fluorescence in situ hybridization and microarrays, has allowed for the identification of cryptic or submicroscopic imbalances, which are not visible under the light microscope. Microarrays have allowed for the identification of numerous new syndromes through a genotype-first approach in which patients with the same or overlapping genomic alterations are identified and then the phenotypes are described. Because many chromosomal alterations are large and encompass numerous genes, the ascertainment of individuals with overlapping deletions and varying clinical features may allow researchers to narrow the region in which to search for candidate genes.

CBL, CBLB, TET2, ASXL1, and IDH1/2 Mutations as Well as Additional Chromosomal Aberrations Constitute Molecular Events Contributing to Malignant Progression In Advanced Philadelphia Chromosome-Positive Disorders.

AbstractAbstract 3396Chronic myeloid leukemia (CML) is characterized by the BCR/ABL fusion gene. However, secondary molecular events leading to accelerated (AP) or blast phase (BP) have not been sufficiently clarified. We hypothesized that, in analogy to other MDS/MPN or MPN, TET2, ASXL1, CBL and IDH family mutations may also occur in CML and contribute as secondary events leading to progression to AP or BP. Similarly, higher resolution of cytogenetic testing by single nucleotide polymorphism array (SNP-A)-based karyotyping may reveal additional chromosomal abnormalities associated with stepwise progression. This study is focused on the combined analysis of chromosomal lesions and mutations associated with AP, BP and Philadelphia chromosome (Ph) positive acute lymphoblastic leukemia (ALL) and the association of these defects with clinical features.We screened TET2, ASXL1, CBL and IDH for mutations in AP (N=14) and BP (N=26) and Ph+ ALL (N=9). Chronic phase (CP) (N=14) and Ph negative ALL (N=9) served as controls. We identified 3 CBL family (9%), 7 TET2 (21%), 2 ASXL1 (6%) and 2 IDH family (6%) mutations in patients with AP and myeloid BP. Subsequently, we also detected a TET2 mutation in a case of Ph+ ALL. None of these mutations were found in patients with CP or Ph negative ALL. We also performed SNP-A-based karyotyping and only included lesions which did not overlap with copy number variations (CNVs) or germ line regions of homozygosity present in any of the controls. 23 gains, 21 losses and 4 regions of somatic UPD lesions were identified. By SNP-A, additional copy number abnormalities, including microdeletions were found in 67% and 50% of patients with AP and BP, respectively. Recurrent lesions were detected on chromosome 1, 8, 9, 17 and 22. Microdeletions on chromosome 17 and 21 involved tumor associated genes NF1 and RUNX1. Deletions flanking the ABL1 and BCR genes were observed in 3 cases with der(22)t(9;22) or der(9)t(9;22) by metaphase cytogenetics. Gains including 1q25.3q41, chromosome 8 and 17q24.3 were found in 3 cases. Regions of UPD included UPD5q, 8q, 11p and 17q but no UPD involving 11q (CBL) and 4q (TET2) regions were found confirming heterozygous nature of the corresponding mutations.Newly detected molecular lesions associated with AP and BP may change the biology and thereby clinical features of affected cases. Overall survival of patients with mutations did not differ from those without mutations. Of note is that BCR/ABL1 kinase domain mutations were detected in 9/10 patients with imatinib resistance. In these 9 cases, 3 TET2 and 2 CBLB mutations were detected (but no mutations in the other genes). In an imatinib-resistant patient without BCR/ABL1 kinase domain mutation, CBL mutation was present. In the patients with TET2 mutations, additional chromosomal lesions were found by SNP-A, significantly more frequently when compared with WT cases (P=0.017). Of the 9 TET2 variants in 8 cases, 7 (78%) were missense substitutions, 1 (11%) was frame shift and 1 (11%) produced a stop codon and were located within the N-terminus as well as in a conserved DSBH 2OG-Fe(II)-dependent dioxygenase domain. The presence of nonsense and frameshift mutations suggests that mutated lesions result in inactivation, consistent with putative tumor suppressor functions, while heterozygous mutations indicate that the wild type allele is not completely protective. Since no TET2 mutations were identified in chronic phase CML, these mutations might represent an additional pathogenic event and contribute to progression. In 3 cases we observed a combination of 2 mutations. Coincidence of CBLB and TET2 mutations in 2 cases suggests that these might cooperate in the evolution of advanced phase of CML. We also found a combination of IDH1 and ASXL1 mutations in a patient with BP, suggesting that both mutations contribute to clonal advantage.In conclusion, while CBL family, ASXL1 and IDH family mutations as well a additional unbalanced chromosomal abnormalities not seen by metaphase cytogenetics can occur in myeloid type advanced phase CML, TET2 mutations were identified in Ph+ ALL, as well as myeloid BP and AP. These mutations likely represent secondary lesions which contribute to either disease progression or more aggressive features and commonly occur in association with imatinib-resistant BCR/ABL mutations. Disclosures:No relevant conflicts of interest to declare.

Is There a Yet Unreported Unbalanced Chromosomal Abnormality without Phenotypic Consequences in Proximal 4p?

Unbalanced chromosomal abnormalities (UBCA) are reported for >50 euchromatic regions of almost all human autosomes. UBCA are comprised of a few megabases of DNA, and carriers are in many cases clinically healthy. Here we report on a partial trisomy of chromosome 4 of the centromere-near region of the short arm of chromosome 4 present as a small supernumerary marker chromosome (sSMC). The sSMC was present in >70% of amnion cells and in 60% of placenta. Further delineation of the size of the duplicated region was done by molecular cytogenetics and array comparative genomic hybridization. Even though the sSMC lead to a partial trisomy of ∼9 megabase pairs, a healthy child was born, developing normally at 1 year of age. No comparable cases are available in the literature. Thus, we discuss here the possibility of having found a yet unrecognized chromosomal region subject to UBCA.

Validation of QF-PCR for Rapid Prenatal Diagnosis of Common Chromosomal Aneuploidies in Korea

Sung-Hee Han, M.D., Jae-Song Ryu, M.S., Jeong-Wook An, M.T., Ok-Kyoung Park, M.T., Hye-Ryoung Yoon, M.D., Young-Ho Yang, M.D. and Kyoung-Ryul Lee, M.D.. J Genet Med 2010;7:59-66. https://doi.org/10.5734/JGM.2010.7.1.59

Evaluation of Array Comparative Genomic Hybridization for Genetic Analysis of Chorionic Villus Sampling from Pregnancy Loss in Comparison to Karyotyping and Multiplex Ligation-Dependent Probe Amplification

The aim of this study was to evaluate the use of array comparative genomic hybridization (aCGH) for genetic analysis of chorionic villus sampling (CVS) from pregnancy loss. aCGH results were compared with results from karyotyping and multiplex ligation-dependent probe amplification (MLPA) analysis to assess the suitability of aCGH as a method for detecting a variety of known chromosomal abnormalities. It was determined which technique gave the most valuable information. Twenty anonymised samples from CVS were analyzed by aCGH, MLPA, and karyotyping. Ten cases were identified as normal by all three methods. Aneuploidy was detected in four cases by all three methods. Partial deletion and duplication was detected in two cases by aCGH and karyotyping but missed by MLPA. In addition, mosaicism was detected by aCGH in 3 of 20 cases missed by MLPA and karyotyping. aCGH is a rapid, automated, reliable, high-resolution technique to diagnose unbalanced chromosomal abnormalities. In this study, aCGH analysis accurately identified all chromosomal abnormalities in CVS from pregnancy loss, suggesting that it is suitable in the clinical setting for prenatal diagnosis.

Prognostic Significance of Unbalanced Chromosome Abnormalities Used by 2008 World Health Organization (WHO) Classification to Define “Acute Myeloid Leukemia (AML) with Myelodysplasia-Related Changes” in Adults: a Cancer and Leukemia Group B (CALGB) Study.

Abstract 2602▪▪This icon denotes an abstract that is clinically relevant.Poster Board II-578One of the major revisions in the 2008 WHO classification of “AML and Related Precursor Neoplasms” is the use of certain cytogenetic abnormalities (abns) as a criterion for inclusion in the “AML with myelodysplasia-related changes” category. These abns include 9 specific reciprocal translocations, 8 unbalanced abns, and complex karyotypes (CK), ie, ≥3 unrelated abns. The clinical features and outcome of patients (pts) with these abns require further study to confirm the appropriateness of their inclusion in this WHO category. Therefore, we evaluated 2,724 consecutive untreated adults meeting criteria for possible inclusion in this WHO category (ie, non-therapy-related AML and not part of the first WHO AML category) in the CALGB cytogenetics database; 516 (19%) pts harbored ≥1 myelodysplasia-related abn and/or CK, and had outcome data available. Their median age was 62 years (y; range, 15–88 y). The 9 reciprocal translocations were very rare, with t(3;5)(q25;q34) found in 6 pts, t(3;21)(q26.2;q22.1) in 2, t(1;3)(p36.3;q21.1) and t(2;11)(p21;q23) in 1 pt each and the remaining 5 translocations not detected. Their rarity precluded further analyses. With the exception of idic(X)(q13), found in 2 pts, the remaining 7 unbalanced abns were more common (Table). Importantly, the abns were not mutually exclusive, ie, ≥2 different abns could co-exist in the same karyotype and/or be part of a CK. Among 453 pts with ≥1 specific unbalanced abn (Table), 62% had CK; the highest % of CK, 89–95%, were seen in the i(17q) or t(17p), −13 or del(13q) and −5 or del(5q) groups and the lowest, only 24%, in del(9q) pts. As a group, non-CK pts had a higher complete remission (CR) rate (P=.002) and longer overall survival (OS; P<.001) than CK pts. This was also the case for OS for most specific abns (Table). Notably, within the non-CK −7 or del(7q) group, −7 pts had worse outcome than del(7q) pts (CR rates, P=.09; OS, P=.002), suggesting that the −7 or 7q- category is not uniform prognostically. Strikingly, pts with del(9q) were younger than pts with other specific myelodysplasia-related unbalanced abns [median age of del(9q) v median age of all others combined, 42 v 63 y, P<.001], and their outcome was better [del(9q) v all others combined: CR rates, 90% v 43%, P<.001; OS, P<.001, 3-y rates, 31% vs. 8%, Figure]. Among 342 pts with CK, those with ≥1 specific myelodysplasia-related unbalanced abn (n=281) had shorter OS than pts without any such abn (n=61; P<.001; 3-y rate, 2% v 20%). We conclude that 1) for most specific myelodysplasia-related unbalanced abns, CK pts do worse than non-CK pts; 2) the presence of specific abns adversely impacts on outcome of CK pts; 3) −7 or 7q- category is not uniform prognostically; 4) del(9q) pts are younger, much less often have CK and their outcome is better than outcome of pts with other unbalanced myelodysplasia-related abns. Consequently, pts with del(9q) appear biologically and clinically different, and their inclusion in the WHO “AML with myelodysplasia-related changes” category should be reconsidered. Future molecular genetic analyses should help characterize each of the cytogenetic subsets within this WHO category further, and might become useful for guiding treatment.Unbalanced myelodysplasia-related abnormalityNo. of pts% with a complex karyotypeNon-complex versus (v) complex karyotypeAgeCR ratesOverall survivalMedian (y)P% attaining a CRP% alive at 3yPAny abnormality4536263v62.9755v40.00222 v2<.001i(17q) or t(17p)1729567v61.0563v39.2725 v1.03−13 or del(13q)599266v62.9060v37.37NA†NA†−5 or del(5q)2268967v63.5725v38.2717 v1<.001del(12p) or t(12p)708161v65.9346v40.768 v2.23−7 or del(7q)2506263v64.8655v40.0219 v3<.001−7*1176866v64.3343v451.00 v3.13del(7q)*1335663v64.3163v34.00231 v3<.001del(11q)164448v50.5644v431.022 v0.15del(9q)292436v59.2695v71.1441 v0<.001*WHO classification does not include -7 or del(7q) as separate categories, but it combines both these aberrations into one category. Here, we provide data for pts with -7 and those with del(7q) separately (italics); pts harboring both -7 and del(7q) are included in the “-7” subgroup.†Too few pts with non-complex karyotype to evaluate estimated overall survival. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Molecular bases of myelodysplastic syndromes: Lessons from animal models

Myelodysplastic syndrome (MDS) is a clonal disorder of hematopietic stem cells characterized by ineffective hematopoiesis, peripheral blood cytopenia, morphologic dysplasia, and susceptibility to acute myeloid leukemia. Several mechanisms have been suggested as causes of MDS: unbalanced chromosomal abnormalities reflecting a gain or loss of chromosomal material, point mutations of transcription factors, and inactivation of p53. However, appropriate animal models that mimic MDS have long been lacking. We recently reported a novel murine model of MDS that recapitulates trilineage dysplasia and transformation to AML. In this review, we summarize the animal models of MDS and discuss the molecular bases of MDS as well as those of leukemia and myeloproliferative disorders (MPD). J. Cell. Physiol. 219: 529-534, 2009. (c) 2009 Wiley-Liss, Inc.

Coexistence of an unbalanced chromosomal rearrangement and spinal muscular atrophy in an infant with multiple congenital anomalies

Unbalanced chromosomal abnormalities are frequent and account for about 10% of all chromosomal abnormalities identified in live births. Diagnosis of a coinherited neuromuscular genetic disorder in these individuals is often challenging based on the severity and variability of the phenotype resulting from the genomic imbalance. Herein, we report on a 4-month-old male with multiple congenital anomalies, craniosynostosis, dysmorphic features, and hypotonia. Karyotype analysis revealed an abnormal male karyotype: 46,XY,der(3)(3;7)(p25;q36), with partial monosomy of 3pter and partial trisomy of 7qter. The targeted array-based comparative genomic hybridization (array-CGH) validated the cytogenetic abnormality, with further elucidation of trisomy of the Sonic Hedgehog (SHH) locus on chromosome 7. Based on the severity of hypotonia in this infant, molecular analysis for spinal muscular atrophy (SMA) was performed and the common homozygous deletion of exon 7 in the survival of motor neuron 1 gene (SMN1) was identified. This case demonstrates the challenges in diagnoses of coexisting genetic disorders in infants with neuromuscular disease. A high index of suspicion in such cases is essential for appropriate case management and family risk assessment.

SNP-Array Based Karyotyping Complements Routine Cytogenetics in Diagnosis and Risk Stratification Schemes of MDS

While current pathomorphologic criteria distinguish MDS, MDS/MPD and MDSderived AML (sAML), these conditions share common unbalanced chromosomal abnormalities highly predictive of prognosis. Reflecting their clinical importance, IPSS is highly influenced by metaphase cytogenetics (MC), the standard for detection of chromosomal abnormalities. Due to its low resolution and need for cell divisions, MC can only detect abnormalities in 50% of patients with MDS, novel technologies have been developed that could improve the diagnostic yield. Among these methods, single nucleotide polymorphism arrays (SNP-A) have been adopted as a cytogenetic platform. SNP-A karyotyping can be performed on interphase cells and allows for detection of smaller lesions as well as for copy-neutral loss of heterozygosity (LOH). As a result, some reference laboratories offer this test for routine cytogenetic diagnostics. However, the clinical relevance of lesions detected by SNP-A remains unclear and, consequently, we designed this comprehensive study to clarify the clinical impact of cytogenetic results generated through a combined application of SNP-A and MC. A cohort of 352 patients (218 MDS, 59 MDS/MPD, 75 sAML) was studied using Affymetrix 250K (N=160), Affymetrix 6.0 (N=190) and both platforms (N=95). Controls included 362 and 118 samples analyzed by 250k and 6.0 arrays, respectively. CNAGv3 or GCv2.1 software was used for analysis. To avoid biological and technical artifacts, known copy number variants as well as areas of LOH<2.5Mba were excluded. All other lesions, if not present on MC, were confirmed in germ line DNA if possible. The median follow-up time was 29 months (95% CI; 21-38 mo) and for many patients serial samples were studied, showing sequential acquisition of chromosomal defects. Overall, the detection rate of chromosomal abnormalities was improved compared to MC (57% vs. 44%; p=.0096), MDS/MPD (66% vs. 39%, p=.0055) and sAML (63% vs. 45%, p=.048). Somatic uniparental disomy (UPD) accounted for a significant proportion of newly detected defects (26% of new lesions). Overall, UPD was detected in 100 patients (78 as the sole and 22 as an additional lesion). Chromosomal lesions were identified in 98/180 with normal MC. In 61% of patients with non-informative MC (N=18), SNP-A demonstrated an abnormal karyotype; those with newly detected lesions showed inferior outcomes in overall survival (OS) [16 vs. 36 mo, p=.03]. Analysis of OS showed that patients with new defects detected by SNP-A and previously normal MC have worse outcomes compared to those in whom normal chromosomes were confirmed (39 vs. 73 mo, p=.03). Moreover, additional lesions also conferred worse prognosis for patients with abnormal karyotype by MC (17 vs. 38 mo, p=.01). This trend was even more pronounced when specific subgroups were analyzed based on OS and event free survival (EFS). For example, detection of new lesions in MDS (OS p=.02), MDS/MPD (OS p=.009, EFS p=.01) or sAML (OS p=.02, EFS p=.008) results in significant worsening of OS and EFS as compared to patients with truly normal cytogenetics. Newly detected lesions allowed for more precise prognostication within established IPSS strata of MDS and MDS/MPD patients. The detection of SNP-A defects negatively impacted OS/EFS in patients with low IPSS (NR vs. 69 mo, p=<.0001; 42 vs. 112 mo, p=<.0001), decreased EFS in Int-1/2 (24 vs. 29 mo; p=<.0001) and decreased OS/ EFS in high IPSS categories (11 vs. 26 mo, p=<.0001; 7 vs. 14 mo, p=<.0001). In sAML, patients with SNP-A lesions, regardless of MC, have worse OS (6 vs. 21 mo, p=.009) and EFS (5 vs. 13 mo, p=.01). In summary, SNP-A karyotyping facilitates detection of lesions which can complement MC and contribute to a better molecular diagnosis. SNPdetected lesions have impact on prognostic parameters which will likely affect future risk stratification schemes and have prognostic significance regardless of MC in sAML. As a result, new molecular subtypes of MDS may be identified and better-defined recurrent lesions will contribute to identification of causative genes.

Be careful with familial unbalanced chromosome abnormalities!

Be careful with familial unbalanced chromosome abnormalities!

Chromosome abnormalities in children, in two Danish counties, born during the period 1967-1978: Clinical data.

Approximately 1 per 1,000 children in a population of 477,000 showed a chromosome abnormality, the expected frequency being 6 per 1,000. The majority of the autosomal abnormalities was trisomy 21 (72 %). The clinical pictures of different autosomal, as well as sex chromosomal abnormalities are described, and different aetiological factors are discussed. Children with the well known autosomal trisomy syndromes were diagnosed to a satisfactory degree, whereas too few were diagnosed of the less well known structural aberrations, deletions, derivatives and unbalanced translocations of all types, as well as of sex chromosome abnormalities. The possibilities of diagnosing more of these chromosome abnormalities are discussed. All autosomal trisomies, unbalanced structural chromosome abnormalities, as well as girls with Turner's syndrome and, to a certain extent, boys with Klinefelter's syndrome could most probably be diagnosed during childhood with a sufficiently intensive cooperation between the general practitioners, obstetricians and paediatricians and the cytogeneticists. It is important to diagnose children with inheritable structural chromosome abnormalities in order to find risk families and to give realistic information, advice, and counselling to the parents, as well as hormone treatment to children with Turner's syndrome and Klinefelter's syndrome at the most suitable age.

Use of high-density SNP-array analysis to identify novel chromosomal abnormalities that predict survival in multiple myeloma

8522 Background: Despite major improvements in the treatment of myeloma over the last decade, disease course is variable due to genetic heterogeneity. Even though cytogenetics is a difficult art in myeloma, chromosomal abnormalities are present in 100% of the patients, and some preliminary data have shown that some chromosomal abnormalities are highly predictive of a short survival. Methods: In order to define the spectrum of unbalanced chromosomal abnormalities in myeloma, we studied a cohort of 192 patients ≤ 65 years of age, homogeneously treated with high dose chemotherapy in the IFM 99 trials, using the Affymetrix 500K SNP arrays. Bone marrow was obtained at diagnosis, and plasma cells were sorted using anti-CD138-coated magnetic beads. In all cases, a plasma cell suspension with a purity > 90% was obtained, and DNA was extracted using standard methods. After labeling, DNA was hybridized on the two Nsp and Sty chips, containing 260,000 SNPs each. Results: As expected, copy number variations were observed in all the cases. The most frequently involved chromosomes were chromosomes 13, 16, 1, 8 and 6. We then performed a prognostic analysis to correlate survival and chromosomal abnormalities. Many previously unreported chromosomal regions were identified. The most frequently lost regions associated with overall survival were 1p, 6q, 8p, 12p, 14q, 16q, 17q, 20p, and 22q. Global analysis revealed a marked heterogeneity in the gains observed in hyperdiploid karyotypes, explaining the inconsistency in the literature regarding the prognostic value of hyperdiploidy. Conclusion: This study represents the largest cohort of patients analyzed with such high-density arrays, enabling the description of a highly confident landscape of chromosomal abnormalities in myeloma. Moreover, since all the 192 patients were treated with a similar high-dose regimen, it allows powerful statistical analysis of the impact of chromosomal gains and losses on response to therapy, event free survival and overall survival. Finally, since all the patients were also annotated for other prognostic parameters such as t(4;14) or beta2-microglobulin, a multivariate prognostic model will be presented. No significant financial relationships to disclose.

Inherited unbalanced structural chromosome abnormalities at prenatal chromosome analysis are rarely ascertained through recurrent miscarriage

To determine the mode of ascertainment of inherited unbalanced structural chromosome abnormalities detected at prenatal chromosome analysis. From the databases of three centres for clinical genetics in the Netherlands, all cases of inherited unbalanced structural chromosome abnormalities detected at prenatal chromosome analysis in the period 1992-2000 were selected. The mode of ascertainment was identified by examining the reason for prenatal chromosome analysis and the reason for parental chromosome analysis of the first structural chromosome abnormality detected within the family. Totally 56 cases of inherited unbalanced structural chromosome abnormalities were detected at prenatal chromosome analysis. Only one case was ascertained through two previous miscarriages (2%). The main modes of ascertainment were a previous child with an unbalanced karyotype (48%), congenital abnormalities at ultrasound examination (20%), and advanced maternal age (9%). The remaining cases had a different mode of ascertainment. Inherited unbalanced structural chromosome abnormalities detected at prenatal chromosome analysis are rarely ascertained through two or more miscarriages.

Chromosome abnormalities in newborn children. Aetiological aspects.

Chromosome examination of 11,148 consecutively liveborn children showed 93 with a chromosome abnormality and 192 with a chromosome variant. There was no significant association between chromosome abnormalities and parental, social and occupational status, except that parents of boys with enlarged Y had a lower social status. Maternal age was higher for children with aneuploid or unbalanced chromosome abnormalities. Low oestriol concentration was more frequent in mothers of children with chromosome abnormalities. Sterility problems were found to a significantly higher degree in parents of children with balanced translocations, and there was a higher frequency of abortions in mothers of boys with enlarged Y chromosome. Oestrogen-gestagen drugs were taken more frequently by mothers of children with aneuploid chromosome abnormalities. Psychotropic drugs, ferro preparations and sulfonamides were taken with a significantly higher frequency among mothers of children with chromosome abnormalities. The frequency of AB Rhesus positive mothers was significantly higher for children with chromosome abnormalities, especially for those with balanced translocations and de novo translocations, than for children with normal karyotypes, whereas mothers of children with sex chromosome abnormalities had a higher frequency of B Rhesus negative blood type. There was also an association between the AB Rhesus negative type and chromosome abnormalities in children.

Cytogenetic and genomic characterization of cell line ARH77

The cell line ARH77 is derived from a patient with plasma cell leukemia and has a complex and continually evolving karyotype. It is frequently used in biological studies of myeloma and plasma cell leukemia, so accurate characterization of the genome is valuable. Here we present a detailed cytogenetic investigation using G-banding and multicolor fluorescence in situ hybridization (M-FISH) in association with assessment of copy number alterations (CNAs) throughout the genome using array-based comparative genomic hybridization (aCGH). In addition to providing an accurate description of the karyotype, this complementary approach highlighted the relative merits of the individual techniques. Conventional cytogenetics and M-FISH indicated the location and types of the major chromosomal changes, whether balanced or unbalanced, and at the same time demonstrated the level of karyotypic evolution between cells. The aCGH profiles reflected the unbalanced chromosomal abnormalities detected by cytogenetics, providing refinement of their genomic breakpoint locations as well as the identification of novel genomic changes. Three aCGH platforms, comprising bacterial artificial chromosome (BAC) or oligonucleotide templates, were available for evaluation. Sixteen CNAs were consistently detected by all three platforms. Novel submicroscopic CNAs (∼0.4 Mb) were detected by the highest resolution platform only, whereas the clones from the BAC arrays provided locus-specific FISH probes for confirmation of CNA.