A multi-center analysis of individuals with a 47,XXY/46,XX karyotype.

INTRODUCTION: Klinefelter syndrome (KS), a sex chromosome aneuploidy, is associated with a 47,XXY chromosomal complement and is diagnosed in ∼1:600 live male births. Individuals with a 46,XX cell line in addition to 47,XXY are less common with a limited number of published case reports. METHODOLOGY: To better understand the implications of a 47,XXY/46,XX karyotype, we conducted a retrospective, multi-center analysis of the cytogenetic findings and associated clinical records of 34 patients diagnosed with this SCA across 14 institutions. RESULTS: Presence of the XX cell line ranged from 5-98% in patient specimens. Phenotypes also exhibited significant heterogeneity with some reporting a single reason for referral and others presenting with a constellation of symptoms, including ambiguous genitalia and ovotestes. Ovotestes were present in 12% of individuals in this cohort, who had a significantly higher percentage of XX cells. Notably, two patients were assigned female sex at birth DISCUSSION: These findings highlight the variability of the clinical phenotypes associated with this SCA as well as the challenges of clinical management for this population. Karyotype or FISH analysis, which offer single-cell resolution, rather than chromosomal microarray or molecular testing, is the ideal test strategy in these instances as mosaicism can occur at low levels.

Patients' ratings of genetic conditions validate a taxonomy to simplify decisions about preconception carrier screening via genome sequencing.

Advances in genome sequencing and gene discovery have created opportunities to efficiently assess more genetic conditions than ever before. Given the large number of conditions that can be screened, the implementation of expanded carrier screening using genome sequencing will require practical methods of simplifying decisions about the conditions for which patients want to be screened. One method to simplify decision making is to generate a taxonomy based on expert judgment. However, expert perceptions of condition attributes used to classify these conditions may differ from those used by patients. To understand whether expert and patient perceptions differ, we asked women who had received preconception genetic carrier screening in the last 3 years to fill out a survey to rate the attributes (predictability, controllability, visibility, and severity) of several autosomal recessive or X-linked genetic conditions. These conditions were classified into one of five taxonomy categories developed by subject experts (significantly shortened lifespan, serious medical problems, mild medical problems, unpredictable medical outcomes, and adult-onset conditions). A total of 193 women provided 739 usable ratings across 20 conditions. The mean ratings and correlations demonstrated that participants made distinctions across both attributes and categories. Aggregated mean attribute ratings across categories demonstrated logical consistency between the key features of each attribute and category, although participants perceived little difference between the mild and serious categories. This study provides empirical evidence for the validity of our proposed taxonomy, which will simplify patient decisions for results they would like to receive from preconception carrier screening via genome sequencing.

Generating a taxonomy for genetic conditions relevant to reproductive planning.

As genome or exome sequencing (hereafter genome-scale sequencing) becomes more integrated into standard care, carrier testing is an important possible application. Carrier testing using genome-scale sequencing can identify a large number of conditions, but choosing which conditions/genes to evaluate as well as which results to disclose can be complicated. Carrier testing generally occurs in the context of reproductive decision-making and involves patient values in a way that other types of genetic testing may not. The Kaiser Permanente Clinical Sequencing Exploratory Research program is conducting a randomized clinical trial of preconception carrier testing that allows participants to select their preferences for results from among broad descriptive categories rather than selecting individual conditions. This paper describes (1) the criteria developed by the research team, the return of results committee (RORC), and stakeholders for defining the categories; (2) the process of refining the categories based on input from patient focus groups and validation through a patient survey; and (3) how the RORC then assigned specific gene-condition pairs to taxonomy categories being piloted in the trial. The development of four categories (serious, moderate/mild, unpredictable, late onset) for sharing results allows patients to select results based on their values without separately deciding their interest in knowing their carrier status for hundreds of conditions. A fifth category, lifespan limiting, was always shared. The lessons learned may be applicable in other results disclosure situations, such as incidental findings.

Atypical presentation of Angelman syndrome with intact expressive language due to low-level mosaicism.

BACKGROUND: Angelman syndrome (AS) occurs due to a lack of expression or function of the maternally inherited UBE3A gene. Individuals with AS typically have significant developmental delay, severe speech impairment with absent to minimal verbal language, gait abnormalities including ataxia, and an incongruous happy demeanor. The majority of individuals with AS also have seizures and microcephaly. Some individuals with mosaic AS have been reported to have expressive language and milder levels of developmental delay. CASE REPORT: We report a male patient presenting with mild to moderate intellectual disability, hyperphagia, obesity, and the ability to communicate verbally. His phenotype was suggestive of Prader-Willi syndrome. However, methylation testing was positive for Angelman syndrome and additional methylation specific multiplex ligation-dependent amplification (MS-MLPA) study revealed low-level mosaicism for AS. CONCLUSION: A broader phenotypic spectrum should be considered for AS as patients with atypical presentations may otherwise elude diagnosis.

Section E9 of the American College of Medical Genetics technical standards and guidelines: fluorescence in situ hybridization.

This updated Section E9 has been incorporated into and supersedes the previous Section E9 in Section E: Clinical Cytogenetics of the 2008 Edition (Revised 02/2007) American College of Medical Genetics Standards and Guidelines for Clinical Genetics Laboratories. This section deals specifically with the standards and guidelines applicable to fluorescence in situ hybridization analysis.

Pharmacogenomic potential of psychiatric medications and CYP2D6.

The ultimate goal in measuring CYP2D6 (or any other CYP450) function or identifying variant alleles is to predict effective therapeutic doses and responses in patients. This is the promise of individualized medicine. By knowing a patient's disposition to drugs, he could be started on appropriate dosing regimens without the extensive trial-and-error period that is common with psychiatric medications. We could also avoid drugs whose metabolism may prove to be problematic, choosing second-line therapies which are metabolized by different, unaffected enzymes. Of course, knowing a genotype is not very useful unless we couple the genotype findings with clinically validated dosing algorithms. Dosing recommendations for PM, EM, IM, and UM patients are beginning to appear in the literature for various classes of drugs but, at present, there are no well-accepted guidelines available. The Food and Drug Administration does encourage the incorporation of pharmacogenomic testing for investigational compounds in the development process. As the notion of PGx becomes more familiar and more clinical trials are completed, evidence-based dosing adjustments should be forthcoming. Although the biochemistry and pharmacology of CYP450 drug metabolism has made huge strides, the application of pharmacogenomics has not yet become commonplace for a number of reasons. Drug metabolism is a complex process, and CYP2D6 may not be the only polymorphic protein involved in a given drug's metabolism. Also, both primary and secondary metabolic pathways exist for drugs, the latter of which may be utilized when other drugs or endogenous compounds occupy the principle pathway. Given the possibility of multiple metabolic pathways, the presence of co-medications, inducers, and inhibitors in the diet and disease changes, predicting drug metabolism in a person remains difficult even when a given CYP450 genotype is obtained. Also there are multiple variants which can be present and consideration must be given as to which variant allele(s) to look for while, at the same time, always considering the cost/benefit ratio of a possible testing algorithm. Despite the numerous uncontrolled variables involved in drug metabolism and the inability for pharmacogenomics to address them all, there remains some promise for CYP2D6 genotyping to at least help physicians hone in on appropriate dose ranges before therapy is initiated or in identifying individuals at metabolic extremes who are at the highest risk for adverse outcomes. Ultimately, if CYP2D6 characterization is shown to be an evidence-based improvement in the practice of psychiatric medicine, laboratorians will need to be prepared for an influx of requests for these tests.

Pediatric T-cell acute lymphoblastic leukemia with aberrations of both MLL loci.

Translocations involving the MLL gene at 11q23 have been implicated in acute lymphoblastic leukemia (ALL), as well as acute myeloid leukemia (AML). Such translocations result in gain of function fusion proteins that drive cell proliferation. Except in cases of T-cell ALL, MLL rearrangement is typically associated with a poor prognosis. We report a case of T-cell ALL with a t(11;19)(q23;p13.3) and deletion of the other chromosome 11 homolog at band q23. Fluorescence in situ hybridization (FISH) analyses confirmed involvement of the MLL loci in both the translocation and deletion. This case is unique in that deletions of 11q23 reported in ALL generally do not involve MLL. We are unaware of a previous report showing rearrangement of the MLL loci on both chromosome 11 homologues.

Cytogenetics caseload survey summary 2012.

In 2004 a cytogenetics caseload and FTE survey was conducted to evaluate cytogenetic laboratory caseload and full-time employee equivalent (FTE) statistics. A similar survey was recently conducted to re-evaluate data. Information gathered by the survey included classification of laboratory type, number of employees according to title, and annual caseload volumes by sample or test type. Workload was evaluated by assigning weighted values to test types based on complexity. Compared with the data from 2004, the current data suggestsgreater complexity in cytogenetics lab testing as well as greater efficiency and productivity.

Analytical performance of the Investigational Use Only Cervista HPV HR test as determined by a multi-center study.

BACKGROUND: Any HPV test designed to be utilized in cervical cancer screening programs should be highly validated both analytically and clinically. OBJECTIVES: The Investigational Use Only (IUO) Cervista HPV HR test is designed to detect 14 high-risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68). The analytical performance of the Cervista HPV HR test was characterized in a multi-center study. RESULTS: Analytical sensitivity for the 14 high-risk HPV types that the test is designed to detect ranged from 1,250 copies to 7,500 copies per reaction depending on HPV type. Accuracy compared to PCR with bi-directional sequencing was 91.4% [95% CI: 86.5 95.0%]. The reproducibility, when tested at three different testing centers, resulted in an overall inter-run reproducibility (between day/within site) agreement of 98.8% [1-sided 95% Confidence Lower Limit = 96.9%] and an overall inter-site reproducibility (between site) agreement of 98.7% [1-sided 95% Confidence Lower Limit = 97.9%]. The Cervista HPV HR test showed no cross-reactivity with DNA from seven non-oncogenic HPV types or 17 different infectious agents at up to 10(7) copies per reaction. CONCLUSIONS: The analytical performance of the Cervista HPV HR test demonstrates sufficient analytical performance for use in cervical cancer screening. As with any clinical laboratory test, analytical characteristics must be evaluated in light of the clinical performance of this assay.

Tetraploidy and 5q deletion in myelodysplastic syndrome: a case report.

Tetraploidy is a very rare cytogenetic abnormality in myelocytic malignancies, and its significance is unclear to date. We report here on a 68-year-old male diagnosed with myelodysplastic syndrome/refractory anemia with excess blasts (MDS/RAEB). Cytogenetic analysis of his bone marrow biopsy at initial clinical presentation and in subsequent studies revealed the presence of two abnormal clones, 92,XXYY and 92,XXYY,del(5)(q13q33). Interphase fluorescence in situ hybridization analysis of abnormal cells confirmed interstitial deletion in 5q, demonstrated predominance of the tetraploid clone and persistent presence of the tetraploid clone with 5q deletion. The patient was not responsive to Revlimid (lenalidomide) treatment, which is routinely used in patients with 5q- syndrome. However, a subsequent course of therapy with the methyl-transferase inhibitor decitabine resulted in clinical and cytogenetic remission. Our data suggest that the unique complex abnormality of tetraploidy and 5q deletion described here for the first time in MDS is characterized by distinct disease etiology, the mechanism of which could involve epigenetic inactivation of gene expression via methylation.

The Prothrombin 20209C>T Sequence Variant: To Test or Not to Test.

Only one mutation in the prothrombin gene (Factor II), 20210G>A, has been definitively associated with an increased risk for venous thrombosis. Using hybridization probe analysis for mutation detection on the LightCycler (Roche Molecular Biochemicals), we identified seven patient samples with atypical melt curve patterns. Sequence analyses of each of these samples revealed heterozygosity for a C to T transition at position 20209. As in other reported cases, each of the apparently unrelated patients was of African-American descent, suggesting that the variant is population specific. Two patients were referred for testing due to a history of stroke, one with a right major coronary artery embolic stroke and the other with a right cerebellar stroke. A third patient had chronic renal failure secondary to hypertension with a reported family history of renal failure. Three patients had a history of multiple pregnancy losses. The last patient had a kidney transplant for end stage renal disease secondary to glomerulonephritis. She was being evaluated for a second transplant, but to our knowledge, had a negative history of venous thrombosis. The prevalence and the clinical significance of the prothrombin 20209C>T mutation is unknown. Recently reported functional studies revealed conflicting results. The clinical utility of testing for and reporting this variant remains unresolved.

HER2 testing: a review of detection methodologies and their clinical performance.

The ERBB2 proto-oncogene, commonly referred to as the human epidermal growth factor receptor-2 (HER2) gene, encodes a 185 kd receptor tyrosine kinase. Overexpression of the protein leads to constitutive activity of the HER2 receptor and breast tumor development through enhanced cell proliferation, survival, motility and adhesion. Overabundance of the HER2 receptor, typically caused by amplification of the HER2 gene, is present in approximately 10-30% of invasive breast cancers, and is associated with an aggressive disease course and decreased disease-free and overall survival in node-positive patients. Tratuzumab, a humanized murine monoclonal antibody, offers a targeted treatment modality for tumors that over express the HER2 protein. Tratuzumab, shown to be effective and initially approved for treatment of metastatic breast cancer, has recently been shown to be very effective in the adjuvant setting. Thus, to offer prognostic information and to direct appropriate treatment it is important to provide accurate laboratory assessment of the status of HER2. This article provides an overview of the methods currently used to assess HER2.

A clinical report of a patient with two abnormal cell lines: 46,XX,del(21)(q22.1) and 47,XX,+3.

Mosaicism for two chromosomally abnormal cell lines in the absence of a normal cell line is exceedingly rare. We report a patient with developmental and growth delay, mild dysmorphic features, a history of hypertension and hepatoblastoma who was found to be mosaic for two chromosomally abnormal cell lines. The cell lines, one containing a terminally deleted chromosome 21, the other trisomy 3, were found in her blood. Fibroblasts and hepatoblastoma tumor cells revealed only the presence of the deleted 21 cell line. Microsatellite marker analysis suggests a mosaic rather than chimeric etiology for the cell lines. This case is exceptional in that the presence of either of these two cell lines alone is uncommon; finding both of these cell lines in an individual appears to be unique.

Triploid mosaicism in a 45,X/69,XXY infant.

We report on an infant referred for chromosome analysis during the neonatal period due to ambiguous genitalia. The genitalia appeared male with bilaterally palpable testes, penoscrotal hypospadias, chordee, and a bifid scrotum. Chromosome analysis and interphase FISH analysis of lymphocytes showed a 45,X karyotype and no evidence for SRY in 200 nuclei examined, respectively. Subsequent chromosome analysis of fibroblasts revealed a 69,XXY karyotype. Molecular studies were carried out to determine the etiology of the chromosome findings. Results indicated that the two cell lines are mosaic rather than chimeric and that the triploidy resulted from delayed dispermy rather than delayed polar body inclusion. To our knowledge this is the first reported living individual with (near) diploid/triploid mosaicism for 45,X/69,XXY.

Submicroscopic deletion 9(q34.3) and duplication 19(p13.3): identified by subtelomere specific FISH probes.

Submicroscopic rearrangements involving chromosome ends are responsible for the unexplained mental retardation and multiple congenital anomalies observed in a number of patients. We have studied a patient with mental retardation, significant microcephaly, alopecia universalis, and other anomalies who carries an unbalanced segregant from a cryptic reciprocal translocation involving chromosomes 9 and 19. FISH studies using subtelomere specific probes revealed a derivative chromosome 9 in which the 9q subtelomeric sequence has been replaced by 19p subtelomeric sequence. As a result, the patient has partial monosomy 9q and partial trisomy 19p. The patient inherited the derivative 9 from his father, who carries a cryptic apparently balanced reciprocal translocation involving the terminal regions of 9q and 19p. This case is exceptional in that reports of rearrangements involving distal chromosome 9q and 19p are rare. This study demonstrates the utility of subtelomere specific FISH probes for detecting cryptic subtelomeric rearrangements in patients with idiopathic mental retardation and normal appearing karyotypes.