Kathleen W. Rao

The genetic architecture of Down syndrome phenotypes revealed by high-resolution analysis of human segmental trisomies

Down syndrome (DS), or trisomy 21, is a common disorder associated with several complex clinical phenotypes. Although several hypotheses have been put forward, it is unclear as to whether particular gene loci on chromosome 21 (HSA21) are sufficient to cause DS and its associated features. Here we present a high-resolution genetic map of DS phenotypes based on an analysis of 30 subjects carrying rare segmental trisomies of various regions of HSA21. By using state-of-the-art genomics technologies we mapped segmental trisomies at exon-level resolution and identified discrete regions of 1.8–16.3 Mb likely to be involved in the development of 8 DS phenotypes, 4 of which are congenital malformations, including acute megakaryocytic leukemia, transient myeloproliferative disorder, Hirschsprung disease, duodenal stenosis, imperforate anus, severe mental retardation, DS-Alzheimer Disease, and DS-specific congenital heart disease (DSCHD). Our DS-phenotypic maps located DSCHD to a <2-Mb interval. Furthermore, the map enabled us to present evidence against the necessary involvement of other loci as well as specific hypotheses that have been put forward in relation to the etiology of DS—i.e., the presence of a single DS consensus region and the sufficiency of DSCR1 and DYRK1A, or APP, in causing several severe DS phenotypes. Our study demonstrates the value of combining advanced genomics with cohorts of rare patients for studying DS, a prototype for the role of copy-number variation in complex disease.

Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism

Cytogenetic imbalances are increasingly being realized as causes of autism. Here, we report a de novo translocation between the short arms of chromosomes 15 and 16 in a female with autism, epilepsy, and global developmental delay. FISH analysis identified a cryptic deletion of approximately 160 kb at the boundary of the first exon and first intron of the 1.7 Mb ataxin‐2 binding protein‐1 (A2BP1) gene, also called FOX1. Quantitative real time PCR (Q‐PCR) analysis verified a deletion of exon 1 in the 5′ promoter region of the A2BP1 gene. Reverse transcription PCR (qRT‐PCR) showed reduced mRNA expression in the individuals lymphocytes, demonstrating the functional consequence of the deletion. A2BP1 codes for a brain‐expressed RNA binding or splicing factor. Because of emerging evidence in the role of RNA processing and gene regulation in pervasive developmental disorders, we performed further screening of A2BP1 in additional individuals with autism from the Autism Genetics Resource Exchange (AGRE) collection. Twenty‐seven SNPs were genotyped across A2BP1 in 206 parent‐child trios and two regions showed association at P ≤ 0.008 level. No additional deletions or clear mutations were identified in 88 probands by re‐sequencing of all exons and surrounding intronic regions or quantitative PCR (Q‐PCR) of exon 1. Although only nominal association was observed, and no obvious causal mutations were identified, these results suggest that A2BP1 may affect susceptibility or cause autism in a subset of patients. Further investigations in a larger sample may provide additional information regarding the involvement of this gene in the autistic phenotype.

Androgenetic/biparental mosaicism causes placental mesenchymal dysplasia

Background: Placental mesenchymal dysplasia (PMD) is a distinct syndrome of unknown aetiology that is associated with significant fetal morbidity and mortality. Intrauterine growth restriction is common, yet, paradoxically, many of the associated fetuses/newborns have been diagnosed with Beckwith-Wiedemann syndrome (BWS). Methods: We report two cases of PMD with high levels of androgenetic (complete paternal uniparental isodisomy) cells in the placenta and document, in one case, a likely androgenetic contribution to the fetus as well. Results: The same haploid paternal complement found in the androgenetic cells was present in coexisting biparental cells, suggesting origin from a single fertilisation event. Conclusions: Preferential allocation of the normal cells into the trophoblast explains the absence of trophoblast overgrowth, a key feature of this syndrome. Interestingly, the distribution of androgenetic cells appears to differ from that reported for artificially created androgenetic mouse chimeras. Androgenetic mosaicism for the first time provides an aetiology for PMD, and may be a novel mechanism for BWS and unexplained intrauterine growth restriction.

Tyrosine Kinase Inhibitor Therapy Induces Remission in a Patient With Refractory EBF1-PDGFRB–Positive Acute Lymphoblastic Leukemia

Introduction Although more than 80% of children who are diagnosed with acute lymphoblastic leukemia (ALL) experience favorable clinical outcomes, a substantial number of children have high-risk disease with an increased probability of relapse and poor prognosis. Genetic alterations, including chromosomal rearrangements and deletions, are important determinants of leukemogenesis and responsiveness to therapy. The ability to identify high-risk patients at the time of diagnosis would enable clinicians to select more targeted therapies and improve survival. For example, patients with BCR-ABL1–positive ALL generally respond poorly to conventional chemotherapy, but outcomes can be improved with the addition of firstand second-generation tyrosine kinase inhibitors (TKIs). Recent genomic analyses have identified a new high-risk subtype of BCR-ABL1–negative ALL with a gene expression profile that is similar to that of BCR-ABL1–positive ALL, deletion of IKZF1 and/or other lymphoid transcriptional regulators, and poor outcome (BCRABL1–like ALL). Approximately 40% of patients with BCR-ABL1– like disease harbor rearrangements that result in aberrant expression of cytokine receptor–like factor 2, and half of these patients also demonstrate activating Janus kinase (JAK1/2) mutations. Recent transcriptome and whole-genome sequencing of BCR-ABL1–like ALL identified a range of genetic alterations that activate kinase signaling, including a recurrent fusion of the B-cell lymphoid transcription factor early B-cell factor 1 to the receptor tyrosine kinase plateletderived growth factor receptor (PDGFRB) on chromosome 5q. It is predicted that the DNA dimerization domain of EBF1 facilitates autophosphorylation and constitutive activation of PDGFRB. The potential for treatment of EBF1-PDGFRB–positive leukemia has not been directly examined in vivo. Here we present a child with EBF1PDGFRB–positive ALL whose disease was refractory to conventional induction chemotherapy but who responded to the addition of imatinib to remission induction therapy, highlighting the potential for TKI therapy to improve the currently poor outcome of patients with BCR-ABL1–like ALL harboring kinase-activating alterations.

Microarray analysis for constitutional cytogenetic abnormalities

Disclaimer: This guideline is designed primarily as an educational resource for health care providers to help them provide quality medical genetic services. Adherence to this guideline does not necessarily ensure a successful medical outcome. This guideline should not be considered inclusive of all proper procedures and tests or exclusive of other procedures and tests that are reasonably directed to obtaining the same results. In determining the propriety of any specific procedure or test, the geneticist should apply his or her own professional judgment to the specific clinical circumstances presented by the individual patient or specimen. It may be prudent, however, to document in the patients record the rationale for any significant deviation from this guideline.

American College of Medical Genetics recommendations for the design and performance expectations for clinical genomic copy number microarrays intended for use in the postnatal setting for detection of constitutional abnormalities

Genomic copy number microarrays have significantly increased the diagnostic yield over a karyotype for clinically significant imbalances in individuals with developmental delay, intellectual disability, multiple congenital anomalies, and autism, and they are now accepted as a first tier diagnostic test for these indications. As it is not feasible to validate microarray technology that targets the entire genome in the same manner as an assay that targets a specific gene or syndromic region, a new paradigm of validation and regulation is needed to regulate this important diagnostic technology. We suggest that these microarray platforms be evaluated and manufacturers regulated for the ability to accurately measure copy number gains or losses in DNA (analytical validation) and that the subsequent interpretation of the findings and assignment of clinical significance be determined by medical professionals with appropriate training and certification. To this end, the American College of Medical Genetics, as the professional organization of board-certified clinical laboratory geneticists, herein outlines recommendations for the design and performance expectations for clinical genomic copy number microarrays and associated software intended for use in the postnatal setting for detection of constitutional abnormalities.

Specific extra chromosomes occur in a modal number dependent pattern in pediatric acute lymphoblastic leukemia.

Children with acute lymphoblastic leukemia (ALL) and high hyperdiploidy (>50 chromosomes) are considered to have a relatively good prognosis. The specific extra chromosomes are not random; extra copies of some chromosomes occur more frequently than those of others. We examined the extra chromosomes present in high hyperdiploid ALL to determine if there were a relation of the specific extra chromosomes and modal number (MN) and if the extra chromosomes present could differentiate high hyperdiploid from near‐triploid and near‐tetraploid cases. Karyotypes of 2,339 children with ALL and high hyperdiploidy at diagnosis showed a distinct nonrandom sequential pattern of gain for each chromosome as MN increased, with four groups of gain: chromosomes 21, X, 14, 6, 18, 4, 17, and 10 at MN 51–54; chromosomes 8, 5, 11, and 12 at MN 57–60; chromosomes 2, 3, 9,16, and 22 at MN 63–67; chromosomes 1, 7 13, 15, 19, and 20 at MN 68–79, and Y only at MN ≥≥80. Chromosomes gained at lower MN were retained as the MN increased. High hyperdiploid pediatric ALL results from a single abnormal mitotic division. Our results suggest that the abnormal mitosis involves specific chromosomes dependent on the number of chromosomes aberrantly distributed, raising provocative questions regarding the mitotic mechanism. The patterns of frequencies of tetrasomy of specific chromosomes differs from that of trisomies with the exception of chromosome 21, which is tetrasomic in a high frequency of cases at all MN. These results are consistent with different origins of high hyperdiploidy, near‐trisomy, and near‐tetrasomy.

MATERNAL UNIPARENTAL DISOMY OF CHROMOSOME 2 AND CONFINED PLACENTAL MOSAICISM FOR TRISOMY 2 IN A FETUS WITH INTRAUTERINE GROWTH RESTRICTION, HYPOSPADIAS, AND OLIGOHYDRAMNIOS

We present a case of maternal uniparental heterodisomy for chromosome 2 (UPD 2) detected after trisomy 2 mosaicism was found on placental biopsy. This case presented prenatally with severe intrauterine growth restriction (IUGR) and oligohydramnios. The diploid newborn had hypospadias and features consistent with oligohydramnios sequence. He died shortly after birth of severe pulmonary hypoplasia. The term placenta had high levels of trisomy 2 in both the trophoblast and the stroma. A comparison of this case with others reported in the literature suggests that the IUGR and oligohydramnios are likely related to placental insufficiency due to the high levels of trisomy 2 present in the trophoblast of the term placenta and the presence of UPD 2 in the diploid placental line.

Monozygotic twins discordant for partial trisomy 1

A 25-year-old primigravida delivered monozygotic twins discordant for multiple anomalies and partial trisomy 1 mosaicism. The phenotype of partial trisomy 1 includes craniofacial, central nervous system, and ocular anomalies. The most likely explanation for these findings is that the translocation occurred after twinning occurred. This observation emphasizes that monozygotic twins are not necessarily genetically identical. They are identical at conception, but subsequent mutation and rearrangement of the genome may cause substantial phenotypic differences.

HER-2 fluorescence in situ hybridization: results from the survey program of the College of American Pathologists.

CONTEXT Fluorescence in situ hybridization (FISH) is a common method used to determine HER-2 status in breast cancer. Limited information is available concerning reproducibility of FISH in determining HER-2 gene amplification. OBJECTIVE To present proficiency testing results of FISH for HER-2 conducted by the Cytogenetics Resource Committee of the College of American Pathologists/American College of Medical Genetics. DESIGN During the past 5 years, unstained sections from 9 invasive breast carcinomas were used for HER-2 FISH proficiency testing, allowing for comparison of FISH results among a large number of laboratories. Additional data were collected using an educational (ungraded) challenge and supplemental questions in the surveys. RESULTS The number of laboratories participating in HER-2 FISH proficiency testing has increased steadily during the past 5 years (from 35 in 2000 to 139 in 2004). Reproducibility of test results among laboratories was excellent for breast tumors with low copy number (no HER-2 amplification) and for breast tumors with high copy number (HER-2 amplification). However, there was considerable variation in interpretation of results for a tumor with low-level HER-2 amplification that was tested on 2 separate occasions. Responses to supplemental questions indicated that there was a need for consensus on the use of a separate equivocal/borderline interpretative category and the need for standardization of cutoff values used to define interpretative categories. CONCLUSIONS The College of American Pathologists proficiency survey programs provide useful information concerning the reproducibility of clinical testing for HER-2 by FISH and reflect clinical interpretation of HER-2 FISH analyses from laboratories across the country.