Pitfalls of using polymerase chain reaction-based assays for JAK2 and CALR exon 9 variant testing in myeloproliferative neoplasms: Knowing when to go the extra mile!

OBJECTIVES

The BCR::ABL1 negative myeloproliferative neoplasms are sequentially tested for JAK2 p.V617F, followed by CALR exon 9 pathogenic variants. Historically, these variants were thought to be mutually exclusive. However, recent reports indicate coexisting JAK2 p.V617F and CALR exon 9 somatic variants.

METHODS

Analysis of JAK2 p.V617F and CALR exon 9 variant was performed by polymerase chain reaction (PCR)-based assays. Subsequent testing was performed on the Genexus integrated sequencer (ThermoFisher) using the Oncomine myeloid assay GX v2.

RESULTS

CALR exon 9 variants were positive in 3 cases, while 2 were positive for JAK2 p.V617F on PCR-based assays. Next-generation sequencing confirmed the JAK2 P.V617F status in all cases. CALR variants resulting in in-frame deletions were identified in 2 cases at a variant allele frequency of 52.16% and 50.91%, while the third case had an intronic CALR variant c.-48G>A at a variant allele frequency of 51.1%. Thus, CALR variants in all 3 cases were interpreted as potentially germline. Of the 228 cases that underwent JAK2 p.V617F and CALR cotesting in the past 2 years, only these 2 cases were positive for both JAK2 p.V617F and CALR exon 9 variants.

CONCLUSIONS

These cases highlight the importance of understanding the pitfalls of molecular techniques in current practice.

Medical students' self-perceived knowledge and clinical comfort with genetics in Pakistan

Pakistan has a high rate of genetic disorders and neonatal mortality concurrent with noted lack of genetic counselors and geneticists. To meet the needs of the patient population, the responsibility of providing clinical genetic services falls on general and specialty physicians. However, their education regarding these essential services is not standardized in medical school curricula nor has it ever been evaluated. The purpose of this work is to describe the self-perceived knowledge, clinical comfort, and perspectives of Pakistani medical students toward their medical genetics' education. A web-based survey was distributed electronically to medical schools around the country. The survey comprised of four sections: (1) participant demographics, (2) self-perceived medical genetics knowledge, (3) level of comfort in applying genetic knowledge and skills, and (4) attitudes toward medical genetics education. Descriptive statistics and a one-way analysis of variance were used for data analysis. Medical students in years 3, 4, and 5 (n = 473) from 25 medical schools participated in this research representing medical education in four Pakistani provinces. Most medical students reported "minimal" to "basic" knowledge of genetic testing methodology (64.7%), cancer genetics (64.9%), prenatal genetic testing (63.02%), and treatment strategies for genetic disease (72.9%). A plurality of students (37%) reported they were uncomfortable with interpreting and communicating genetic test results to patients. Medical students also expressed dissatisfaction with their medical genetics (40%) and genetic counselors training (42%). The self-perceived knowledge and clinical comfort with genetics among Pakistani medical students was limited, especially regarding genetic testing. A significant portion (74.5%) expressed desire for additional genetics education during medical school to aid in their role as future physicians. It is important for physicians-in-training to have a solid understanding of genetic concepts, technologies, and genetic counseling to best support their patients. As endorsed by the participating medical students, this study supports inclusion of more robust genetics' education into Pakistan's medical school curricula.

PIK3CA-related overgrowth spectrum (PROS) presenting as isolated macrodactyly

PIK3CA-related overgrowth spectrum (PROS) is a heterogeneous group of diseases, with varied clinical presentations ranging from isolated segmental overgrowths to megalencephaly and vascular malformations, all resulting from post-zygotic activating mutations in PIK3CA. Isolated macrodactyly of upper limb is extremely rare, accounting only for 0.9%-1% of all congenital anomalies of the upper limb. This report describes a case of congenital, isolated, nonprogressive macrodactyly of the right index finger and thumb, in an adult patient that was treated with debulking surgery. The microscopic features were compatible with lipomatosis of nerve. Due to the prompt and pertinent molecular testing, which identified a somatic PIK3CA variant, c.3140A > G, p.H1047R., the case was classified as a PROS. The availability of mTOR inhibitors offers additional treatment possibilities in cases with progressive disease. This case report highlights the importance of molecular testing to identify PROS, to further the knowledge of this continually expanding entity.

Identifying the current status and future needs of clinical, educational, and laboratory genetics services in Pakistan: a web-based panel discussion

While the prevalence of genetic disorders has been well documented in the Muslim-majority, low-socioeconomic country of Pakistan, the provision of medical genetic services remains limited and cost-prohibitive to the masses in the country. With the objective of identifying gaps in the provision of medical genetics services as perceived by the healthcare providers and the general public, the Pakistani Society of Medical Genetics and Genomics (PSMG) organized a needs assessment webinar on December 6, 2020, titled, "A Vibrant Discussion on the Current Status and Future Needs of Medical Genetic Services in Pakistan." The objectives of the webinar were (1) to explore the current availability of medical genetics services, (2) to identify areas in clinical genetics delivery models needed to improve the state of medical genetics in the country, and (3) to garner the interest in such provisions from the expert and lay audience. The webinar consisted of a moderator-led, structured interview of an expert panel including the following topics: (1) postgraduate clinical genetics and genetic counseling training programs, (2) medical genetics clinics and formal genetic counseling services), (3) clinical genetic testing and (4) patient support and advocacy groups. The webinar was followed by a short, web-based survey completed by 35 of the 60 attendees. The results of this survey indicated overwhelming support for establishing formal genetic counseling educational opportunities (91.6%) and increasing the availability of genetic testing (100%). This report further summarizes the opinions and recommendations of the panelists and the audience survey results.

Identifying unnecessary duplicate genetic testing in a large medical center

Introduction

Genetic testing has become ubiquitous in clinical medicine and plays an important role in making diagnoses and guiding treatment plans. Indiscriminate use of these tests can cause duplicate testing, which is typically not indicated because results from repeated constitutional molecular genetic testing should not change over time. Thus, duplicate genetic testing often represents inappropriate test utilization that can contribute an unnecessary burden on the laboratory and health care system.

Objective

The purpose of our study is to determine the incidence of duplicate testing of in-house genetic testing offered at a large medical center, which includes cystic fibrosis, factor V Leiden, prothrombin G20210A, methylenetetrahydrofolate reductase (MTHFR) C677T, and MTHFR A1298C, and to develop a tool to identify and block duplicate testing.

Methods

We retrospectively analyzed internal laboratory databases of all cystic fibrosis (n = 36164), factor V Leiden (n = 3264), prothrombin G20210A (n = 2890), MTHFR C667T (n = 1451), and MTHFR A1293C (n = 1290) testing performed at the molecular pathology laboratory at a large medical center from either January 2010 or January 2014 to July 2019. We analyzed and cleaned the databases with the R programming language, and we developed a prototype web-based app to proactively identify duplicate test requests with the Shiny R package.

Results

From January 2010 to July 2019, 3535 (9.8%) of the 36164 cystic fibrosis tests performed were duplicate tests for 3257 unique patients. Of these duplicate cystic fibrosis tests, 2997 were repeated once in the same patient, 244 were repeated twice in the same patient, 14 were repeated three times in the same patient, and 2 were repeated four times in the same patient. From January 2014 to July 2019, 99 (3.0%) of the 3264 factor V Leiden tests, 86 (3.0%) of the 2890 prothrombin G20210A tests, 49 (3.4%) of the 1451 MTHFR C667T, and 46 (3.6%) of the 1290 MTHFR A1298C tests performed were duplicate tests.

We developed a proof-of-concept Shiny web-browser app that provides a user-friendly interface to determine if a patient has been previously tested in the molecular pathology lab. This app operates locally on a laboratory computer and uses spreadsheets automatically exported from the electronic medical record. These features allow for the app to be deployed quickly without needing to be integrated into the electronic medical record.

Conclusions

The results of this study indicate that unnecessary duplicate testing represents a small but significant proportion of genetic testing performed by the molecular pathology laboratory. Duplicate testing occurred more frequently with cystic fibrosis testing, which reflects its high volume at the medical center. Deployment of web-based apps using Shiny can provide straightforward and efficient tools for reducing duplicate tests.

Karyotypic complexity, TP53 pathogenic variants, and increased number of variants on Next-Generation Sequencing are associated with disease progression in a North American Adult T-Cell Leukemia/Lymphoma cohort

INTRODUCTION

Adult T-Cell Leukemia/Lymphoma (ATLL) is an aggressive T-cell malignancy without known characteristic cytogenetic abnormalities. Recurrent mutations in TP53, APC, and epigenetic and histone-modifying genes have been identified in North American ATLL. Their roles in disease progression are not yet fully elucidated.

METHODS

We studied the cytogenetic and Next-Generation Sequencing (NGS) findings of the North American ATLL cohort at our institution and compared the findings with Japanese and other North American cohorts. We also analyzed the genetic variants in TP53, APC, and histone-modifying genes and investigated the impact of their mutations on the number of mutations via NGS in ATLL.

RESULTS

Cases with more than 6 chromosomal breaks (n = 13) had significantly shorter overall survival compared to cases with fewer chromosomal breaks (n = 7) (P = .0007). Cases with breaks on chromosome 3q (n = 4) exhibited worse survival compared to the rest of the cases (n = 16) (P = .012). Chromosomal abnormalities on 3q, 14q, 1q, 1p, and 17q are likely primary changes in ATLL based on frequency and association with prognosis. The average number of mutations via NGS was significantly higher in cases with mutations in TP53 (n = 8) (P = .020) as well as APC (n = 6) (P = .024) compared to cases without mutations in these genes. All TP53 variants were pathogenic missense and truncating mutations in COSMIC database.

CONCLUSION

Cytogenetic and NGS methods are useful tools to monitor disease progression in indolent ATLL and assess prognosis in aggressive ATLL.

Enhanced Carrier Screening for Spinal Muscular Atrophy: Detection of Silent (SMN1: 2 + 0) Carriers Utilizing a Novel TaqMan Genotyping Method

BACKGROUND

Individuals whose copies of the survival motor neuron 1 (SMN1) gene exist on the same chromosome are considered silent carriers for spinal muscular atrophy (SMA). Conventional screening for SMA only determines SMN1 copy number without any information regarding how those copies are arranged. A single nucleotide variant (SNV) rs143838139 is highly linked with the silent carrier genotype, so testing for this SNV can more accurately assess risk to a patient of having an affected child.

METHODS

Using a custom-designed SNV-specific Taqman genotyping assay, we determined and validated a model for silent-carrier detection in the laboratory.

RESULTS

An initial cohort of 21 pilot specimens demonstrated results that were 100% concordant with a reference laboratory method; this cohort was utilized to define the reportable range. An additional 177 specimens were utilized for a broader evaluation of clinical validity and reproducibility. Allelic-discrimination analysis demonstrated tight clustering of genotype groupings and excellent reproducibility, with a coefficient of variation for all genotypes ranging from 1% to 4%.

CONCLUSION

The custom-developed Taqman SNV genotyping assay we tested provides a rapid, accurate, and cost-effective method for routine SMA silent-carrier screening and considerably improves detection rates of residual risk for SMA carriers.

De novo mosaic and partial monosomy of chromosome 21 in a case with superior vena cava duplication

Background

Full or partial monosomy of chromosome (chr) 21 is a very rare abnormal cytogenetic finding. It is characterized by variable sizes and deletion breakpoints on the long arm (q) of chr 21 that lead to a broad spectrum of phenotypes that include an increased risk of birth defects, developmental delay and intellectual deficit.

Case presentation

We report a 37-year-old G1P0 woman initially screened by non-invasive prenatal testing with no positive findings that was followed by an 18-week anatomy scan with a fetal finding of duplication of the superior vena cava (SVC). The medical and family history was otherwise uneventful. After appropriate genetic counseling, amniocentesis was performed to evaluate suspected chromosomal anomalies.

Conclusions

Interphase fluorescent in situ hybridization revealed loss of one chr 21 signal that was further delineated by chromosomal microarray analysis on uncultured amniocytes as a terminal 10 Mb deletion on chr 21q. Karyotype and microarrays on cultured amniocytes showed two cell lines for a mosaic 21q terminal deletion and monosomy 21. The combined molecular cytogenetics results reported following the ISCN 2016 guideline as mos 46,XX,del(21)(q22)dn[20]/45,XX,-21dn[10].nuc ish(D21S342/D21S341/D21S259x1)[100].arr[GRCh37] 21q11.2q22.12(15412676_36272993)x1~2,21q22.12q22.3(36431283_47612400)x1. Parental chromosomal analysis revealed normal karyotypes. Thus, this was a de novo mosaic full and partial monosomy of chr 21 in a case with SVC duplication. Despite the association of congenital heart disease with monsomy 21 we could not find any published literature or online databases for this cytogenetic abnormality. The patient terminated the pregnancy following the abnormal molecular cytogenetic results due to the possible challenges the baby would face if carried to term.

The value of manipulation of displaced distal radius fractures in the emergency department

The aim of this study was to report the success of maintaining reduced distal radius fractures with cast immobilisation and analyse risk factors for redisplacement. A retrospective analysis of distal radius fracture manipulated between April 2011 and 2013 was conducted. Age, gender, fracture classification, ulna fracture, dorsal comminution and volar alignment were recorded. Reduction and redisplacement were measured using Sarmiento's modification of Lidstrom's system. 110 patients were included ; mean age 62.8 years and 83.4% female. The AO classification was used to grade initial fractures A2 (44%), A3 (25%), C1 (20%) and C2 (10%). 86.4% of cases were improved following manipulation, although 48.4% redisplaced and 27.4% required surgical intervention. The radial length (60%) was harder to maintain than dorsal alignment (44%) in cases of redisplacement. Successful alignment of the volar cortices was associated with a statistically significant reduction in redisplacement (p = 0.024). Manipulation of distal -radius fractures is initially beneficial but half of cases redisplace.

Mycosis fungoides with epidermal mucinosis: a variant of mycosis fungoides with a spongiosis-like pattern

BACKGROUND

The histopathologic diagnosis of mycosis fungoides (MF) has classically relied on the presence of atypical epidermotropic T-lymphocytes predominating over spongiosis. However, in some cases of MF, prominent epidermal mucinosis in a spongiosis-like pattern mimics a spongiotic dermatitis. To our knowledge, only one series in the literature has thus far recognized the presence of epidermal mucinosis in MF.

METHODS

We evaluated 30 skin biopsies from 18 patients with the clinical diagnosis of MF, which fulfilled all histopathologic criteria for patch- or plaque-stage MF, but also showed epidermal mucinosis in a spongiosis-like pattern. A total of 15 specimens were studied by immunohistochemistry, and seven were tested for T-cell receptor (TCR) gene rearrangements. Twenty biopsies of spongiotic dermatitides were included as controls.

RESULTS

We confirmed the presence of epidermal mucinosis in all 30 cases of MF with a spongiosis-like pattern based on histopathologic criteria and the colloidal iron stain for mucin. Immunohistochemistry in 15 specimens showed significant loss of pan-T-cell antigens CD5 (10/15) and CD7 (14/15); and TCR clonality was detected in 7 specimens from 6 patients, supporting the diagnosis of MF.

CONCLUSIONS

We report helpful histopathologic criteria for distinguishing MF with epidermal mucinosis in a spongiosis-like pattern from spongiotic dermatitis.

A comparison of magnetic resonance arthrography and arthroscopic findings in the assessment of anterior shoulder dislocations

OBJECTIVE

The aim of this study is to establish the sensitivity and specificity of MRA in the investigation of patients with traumatic anterior shoulder dislocations.

MATERIALS AND METHODS

A retrospective analysis of consecutive patients undergoing both magnetic resonance arthrography and arthroscopic assessment after a traumatic anterior shoulder dislocation between January 2011 and 2014 was performed. Demographic data were collected from electronic records. Images were interpreted by 8 musculoskeletal radiologists and patients were treated by 8 consultant orthopaedic surgeons. Arthroscopic findings were obtained from surgical notes and these findings were used as a reference for MRA. The sensitivity, specificity, and positive predictive value were calculated for the different injuries.

RESULTS

Sixty-nine patients underwent both an MRA and shoulder arthroscopy during the study period; however, clinical notes were unavailable in 9 patients. Fifty-three patients (88 %) were male, the mean age was 28 years (range 18 to 50) and 16 subjects (27 %) had suffered a primary dislocation. The overall sensitivity and specificity of MRA to all associated injuries was 0.9 (CI 0.83-0.95) and 0.94 (CI 0.9-0.96) retrospectively. The lowest sensitivity was seen in osseous Bankart 0.8 (CI 0.44-0.96) and superior labral tear (SLAP) lesions 0.5 (CI 0.14-0.86). The overall positive predictive value was 0.88 (CI 0.76-0.91) with the lowest values found in rotator cuff 0.4 (CI 0.07-0.83) and glenohumeral ligament (GHL) lesions 0.29 (CI 0.05-0.7).

CONCLUSION

Magnetic resonance angiography has a high sensitivity when used to identify associated injuries in shoulder dislocation, although in 8 patients (13 %) arthroscopy identified an additional injury. The overall agreement between MRA and arthroscopic findings was good, but the identification of GHL and rotator cuff injuries was poor.

A de novo 10.79 Mb interstitial deletion at 2q13q14.2 involving PAX8 causing hypothyroidism and mullerian agenesis: a novel case report and literature review

Reports of interstitial deletions involving proximal long arm of chromosome 2 are limited. Based on early chromosomal analysis studies, the phenotypic consequence of deletions at the ancestral chromosome fusion site at chromosome 2q13q14.1 remains unclear. A recurrent 1.71 Mb deletion at 2q13 has recently been proposed as a new genomic disorder, associated with an increased risk of intellectual disability and craniofacial dysmorphism. Herein, we report the case of a 12 year-old girl with unique clinical features including global developmental delay, mullerian agenesis, and hypothyroidism associated with a normal size and position of the thyroid gland, as well as negative thyroid antibodies. Microarray-based comparative genomic hybridization study revealed a de novo 10.79 Mb deletion at 2q13q14.2 (111,548,932–122,336,492), which involves more than 88 UCSC genes, 38 of which are OMIM genes, 7 of which are disease-causing and 3 of which (including GLI2, IL1B and PAX8) show a dominant inheritance pattern.. Interestingly, PAX8 (chr2:113,973,574–114,036,498), a member of the paired-box gene family, is essential for the formation of thyroxine-producing follicular cells. Autosomal dominant transmission of congenital thyroid hypoplasia due to loss-of-function mutation of PAX8 suggests a possible haploinsufficiency effect. Additionally, PAX8 is also expressed in the tissue primordia that form both the mullerian duct derivatives and the upper urinary tracts. A recent study has associated a novel PAX8 mutation with a severe form of hypothyroidism and abnormalities in the urogenital tract. Taken together, the unique clinical manifestation seen in this patient could be attributed to the heterozygous deletion of PAX8 gene. A prospective investigation is merited to fully evaluate the pathogenic effect of the interstitial deletion of 2q13q14.2.

Overexpression of ZNF342 by juxtaposition with MPO promoter/enhancer in the novel translocation t(17;19)(q23;q13.32) in pediatric acute myeloid leukemia and analysis of ZNF342 expression in leukemia

We report a novel translocation t(17;19)(q22;q13.32) found in 100% of blast cells from a pediatric acute myeloid leukemia (AML) patient. Fluorescence in situ hybridization and vectorette polymerase chain reaction were used to precisely map the chromosomal breakpoint located on the derivative chromosome 17 at 352 bp 5' of MPO, encoding myeloperoxidase a highly expressed protein in myeloid cells, and 2,085 bp 5' of ZNF342 on 19q, encoding a transcription factor expressed in human stem cells and previously implicated in mouse models of leukemia. Analysis of RNA levels from the patient sample revealed significant overexpression of ZNF342, potentially contributing to AML formation. This is the first report of a translocation in myeloid leukemia occurring only in the promoter/enhancer regions of the two genes involved, similar to translocations commonly found in lymphoid malignancies. Analysis of ZNF342 protein levels in a large dataset of leukemia samples by reverse phase protein array showed that higher levels of ZNF342 expression in acute lymphoblastic leukemia was associated with poorer outcome (P = 0.033). In the myeloid leukemia samples with the highest ZNF342 expression, there was overrepresentation of FLT3 internal tandem duplication (P = 0.0016) and AML subtype M7 (P = 0.0002). Thus, overexpression of ZNF342 by translocation or other mechanisms contributes to leukemia biology in multiple hematopoietic compartments.

Overexpression of Eg5 causes genomic instability and tumor formation in mice

Proper chromosome segregation in eukaryotes is driven by a complex superstructure called the mitotic spindle. Assembly, maintenance, and function of the spindle depend on centrosome migration, organization of microtubule arrays, and force generation by microtubule motors. Spindle pole migration and elongation are controlled by the unique balance of forces generated by antagonistic molecular motors that act upon microtubules of the mitotic spindle. Defects in components of this complex structure have been shown to lead to chromosome missegregation and genomic instability. Here, we show that overexpression of Eg5, a member of the Bim-C class of kinesin-related proteins, leads to disruption of normal spindle development, as we observe both monopolar and multipolar spindles in Eg5 transgenic mice. Our findings show that perturbation of the mitotic spindle leads to chromosomal missegregation and the accumulation of tetraploid cells. Aging of these mice revealed a higher incidence of tumor formation with a mixed array of tumor types appearing in mice ages 3 to 30 months with the mean age of 20 months. Analysis of the tumors revealed widespread aneuploidy and genetic instability, both hallmarks of nearly all solid tumors. Together with previous findings, our results indicate that Eg5 overexpression disrupts the unique balance of forces associated with normal spindle assembly and function, and thereby leads to the development of spindle defects, genetic instability, and tumors.

A constitutional balanced t(3;8)(p14;q24.1) translocation results in disruption of the TRC8 gene and predisposition to clear cell renal cell carcinoma

Studying the molecular basis of familial renal cell carcinoma (RCC) has allowed identification of novel RCC genes involved in the pathogenesis of both inherited and sporadic RCC. We describe a constitutional balanced t(3;8)(p14;q24.1) translocation found in a brother and sister with bilateral clear cell RCC (CC-RCC) diagnosed in their forties. Consistent with a prior report, we demonstrated by RT-PCR of RNA from lymphoblastoid cells fusion mRNAs derived from the fragile histidine triad (FHIT) at 3p14 and TRC8 at 8q24.1 in both affected siblings. Cytogenetic analysis of a CC-RCC tumor from the affected sister from short-term tumor cell culture showed both diploid and pseudotetraploid populations containing the translocation and normal appearing chromosomes 3 and 8. Fluorescent in situ hybridization using bacterial artificial chromosomes containing sequences from the FHIT and TRC8 genes demonstrated normal FHIT signals and TRC8 signals on nontranslocated chromosomes in the constitutional blood sample, but the TRC8 signal was absent in a subset of diploid and pseudotetraploid cells from the tumor. The tumor also contained a heterozygous VHL frameshift somatic mutation. These results confirm that balanced translocations disrupting the TRC8 and FHIT genes result in an increased genetic susceptibility for bilateral CC-RCC. The presence of diploid and tetraploid tumor cells with and without TRC8 deletions on the nontranslocated chromosome suggest that loss of the remaining normal allele of TRC8 may contribute to tumor development at later stages.

Stromal fibroblasts present in invasive human breast carcinomas promote tumor growth and angiogenesis through elevated SDF-1/CXCL12 secretion

Fibroblasts often constitute the majority of the stromal cells within a breast carcinoma, yet the functional contributions of these cells to tumorigenesis are poorly understood. Using a coimplantation tumor xenograft model, we demonstrate that carcinoma-associated fibroblasts (CAFs) extracted from human breast carcinomas promote the growth of admixed breast carcinoma cells significantly more than do normal mammary fibroblasts derived from the same patients. The CAFs, which exhibit the traits of myofibroblasts, play a central role in promoting the growth of tumor cells through their ability to secrete stromal cell-derived factor 1 (SDF-1); CAFs promote angiogenesis by recruiting endothelial progenitor cells (EPCs) into carcinomas, an effect mediated in part by SDF-1. CAF-secreted SDF-1 also stimulates tumor growth directly, acting through the cognate receptor, CXCR4, which is expressed by carcinoma cells. Our findings indicate that fibroblasts within invasive breast carcinomas contribute to tumor promotion in large part through the secretion of SDF-1.

A patient with isochromosome 18q, radial-thumb aplasia, thrombocytopenia, and an unbalanced 10;18 chromosome translocation

We report on the clinical and cytogenetic findings in a newborn with a de novo isochromosome 18q. Radial/thumb aplasia and thrombocytopenia were significant features in addition to multiple congenital anomalies. Comparison with reported cases suggests that the genes for such features are located on the 18q arm. An additional finding of a non-reciprocal translocation between chromosome 18p telomere and chromosome 10q telomere was also observed in a majority of cells examined. This additional rearrangement likely has minimal phenotypic consequences, but does raise the possibility that cryptic translocations of telomeric ends of the deleted arm in isochromosome cases may be more common than appreciated.

Loss of Heterozygosity Occurs via Mitotic Recombination in Trp53+/− Mice and Associates with Mammary Tumor Susceptibility of the BALB/c Strain

Loss of heterozygosity (LOH) occurs commonly in cancers causing disruption of tumor suppressor genes and promoting tumor progression. BALB/c-Trp53(+/-) mice are a model of Li-Fraumeni syndrome, exhibiting a high frequency of mammary tumors and other tumor types seen in patients. However, the frequency of mammary tumors and LOH differs among strains of Trp53(+/-) mice, with mammary tumors occurring only on a BALB/c genetic background and showing a high frequency of LOH, whereas Trp53(+/-) mice on a 129/Sv or (C57BL/6 x 129/Sv) mixed background have a very low frequency of mammary tumors and show LOH for Trp53 in only approximately 50% of tumors. We have performed studies on tumors from Trp53(+/-) mice of several genetic backgrounds to examine the mechanism of LOH in BALB/c-Trp53(+/-) mammary tumors. By Southern blotting, 96% (24 of 25) of BALB/c-Trp53(+/-) mammary tumors displayed LOH for Trp53. Karyotype analysis indicated that cells lacking one copy of chromosome 11 were present in all five mammary tumors analyzed but were not always the dominant population. Comparative genomic hybridization analysis of these five tumors indicated either loss or retention of the entire chromosome 11. Thus chromosome loss or deletions within chromosome 11 do not account for the LOH observed by Southern blotting. Simple sequence length polymorphism analysis of (C57BL/6 x BALB/c) F1-Trp53(+/-) mammary tumors showed that LOH occurred over multiple loci and that a combination of maternal and paternal alleles were retained, indicating that mitotic recombination is the most likely mechanism of LOH. Nonmammary tumors of BALB/c mice also showed a high frequency of LOH (22 of 26, 85%) indicating it was not a mammary tumor specific phenomenon but rather a feature of the BALB/c strain. In (C57BL/6 x BALB/c) F1-Trp53(+/-) mice LOH was observed in 93% (13 of 14) of tumors, indicating that the high frequency of LOH was a dominant genetic trait. Thus the high frequency of LOH for Trp53 in BALB/c-Trp53(+/-) mammary tumors occurs via mitotic recombination and is a dominant genetic trait that associates with the occurrence of mammary tumors in (C57BL/6 x BALB/c) F1-Trp53(+/-) mice. These results further implicate double-strand DNA break repair machinery as important contributors to mammary tumorigenesis.

Cytogenetic Abnormalities in Products of Conception: A Relationship Revisited

OBJECTIVES

Cytogenetic evaluation of product of conception (POC) is essential to determine the cause of pregnancy loss and aid the prenatal diagnosis of subsequent pregnancies. The purpose of this study is twofold. (1) To profile cytogenetic abnormalities, their relationship with maternal and gestational age and analyze sex ratios in our case series of 2052 consecutive samples of POC referred to the Baystate Medical Center, Laboratory Genetics between January 1992 and January 1999. (2) To present a comprehensive review of such data published in the last 15 years, in order to study temporal differences in the above parameters and make this information readily available for cytogeneticists and genetic counselors.

MATERIALS AND METHODS

Data was entered and analyzed in Epi Info version 6.0 using the Z-test, chi-square test of significance and linear correlation coefficient.

RESULTS AND CONCLUSIONS

The profile of cytogenetic abnormalities detected in POC has not changes significantly over time. The mean maternal age in our study (overall and for trisomies) was higher than that reported previously, which is consistent with the noted trend of increasing age at pregnancy in recent years. Our study provides evidence that abnormal karyotypes are aborted earlier and that tetraploidies have the least survival amongst all abnormalities. The higher mean gestational age for trisomic abortions in our study, as compared with previously reported figures, can be attributed to the increasing practice of active maternal screening with subsequent therapeutic abortions. Analysis of sex ratios may reaffirm a female specific developmental disadvantage in early stages of pregnancy.

Attenuated phenotype in a child with trisomy for 1q due to unbalanced X;1 translocation [46,X,der(X),t(X;1)(q28;q32.1)]

We report a case of an X;1 translocation in a 9-month-old female infant with mild dysmorphic features and developmental delay. High-resolution chromosome analysis revealed a de novo, unbalanced translocation between chromosomes X and 1 [46,X,der(X),t(X;1)(q28;q32.1)]. Breakpoints on the derivative X and the size of the translocated segment have been defined by fluorescence in situ hybridization (FISH) with Xq and 1q specific probes. The rearrangement in this patient results in monosomy for Xq28-qter and trisomy for 1q32.1-qter. Replication studies demonstrated late replication of the derivative X in 80% of the observed cells, with the exception of 20% of the cells where X inactivation failed to spread into the translocated 1q segment. Patients with pure trisomy for the distal segment of 1q present a considerably more severe phenotype compared to that seen in our patient, including facial dysmorphisms, urogenital and cardiac anomalies. We suggest that the absence of many of the characteristic features for trisomy 1q in our patient, may reflect a mosaic pattern of inactivation of the translocated autosomal segment on the derivative X chromosome.

Overexpression of MAGE/GAGE genes in paclitaxel/doxorubicin-resistant human cancer cell lines

Previous studies directed at identifying paclitaxel resistance genes in a paclitaxel-resistant subclone of the human ovarian cancer cell line SKOV-3 identified a novel cancer testis antigen, Taxol resistance-associated gene 3 (TRAG-3). Because investigation suggested that TRAG-3, located on chromosome Xq28, does not directly participate in the paclitaxel-resistant phenotype, it was hypothesized that TRAG-3 might be linked to a neighboring gene that is directly involved in the drug-resistant phenotype, or alternatively, overexpression of TRAG-3 might be attributable to coregulation with other cancer testis antigens. To distinguish between these two hypotheses, expression of the genes that flank TRAG-3 was evaluated, namely the Centrin 2 gene and several members of the MAGE gene cluster. Northern analysis demonstrates overexpression of MAGE2 but not Centrin 2. Extension of this analysis to other neighboring and non-neighboring representative cancer testis antigens reveals overexpression of MAGE3, MAGE6, MAGE11, and MAGE12, as well as GAGE-2, GAGE-4, GAGE-5, GAGE-6, and GAGE-7 (clustered on Xp11) in SKOV-3(TR), as compared with SKOV-3. In addition, Affymetrix-based analysis of gene expression in SKOV-3 subclones with variable paclitaxel resistance demonstrates MAGE gene overexpression occurs early in the development of the paclitaxel-resistant phenotype, whereas GAGE gene overexpression occurs somewhat later. Evaluation of additional breast and ovarian cancer cell lines reveals MAGE/GAGE overexpression in both paclitaxel- and doxorubicin-resistant cell lines, whereas gemcitabine-resistant subclones of several ovarian cancer cell lines, including SKOV-3(GR), reveals no change in MAGE/GAGE expression. To determine whether MAGE gene overexpression contributes directly to the drug-resistant phenotype, MAGE2 or MAGE6, cDNA was introduced into the paclitaxel-sensitive human ovarian cancer cell line OVCAR8. 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cytotoxicity analysis of both MAGE2 and MAGE6 transfectants demonstrates a 4-fold increase in resistance to paclitaxel and 2-fold increase in resistance to doxorubicin but not to other drugs, such as topotecan and cisplatin, through a nonmultidrug resistance-1 mechanism. MAGE2 or MAGE6 overexpression also induces a growth advantage in OVCAR8-transfected cells. These studies suggest that the in vitro acquisition of paclitaxel and doxorubicin resistance can be associated with increased expression of a variety of both neighboring and non-neighboring cancer testis antigens genes. This does not appear to be a consequence of random genetic instability or genomic amplification of the X chromosome. These antigens, because of limited expression in normal tissues, may be suitable targets for immunotherapy and novel therapeutic strategies in the treatment of chemotherapy-resistant epithelial tumors.

Cloned transchromosomic calves producing human immunoglobulin

Human polyclonal antibodies (hPABs) are useful therapeutics, but because they are available only from human donors, their supply and application is limited. To address this need, we prepared a human artificial chromosome (HAC) vector containing the entire unrearranged sequences of the human immunoglobulin (hIg) heavy-chain (H) and lambda (lambda) light-chain loci. The HAC vector was introduced into bovine primary fetal fibroblasts using a microcell-mediated chromosome transfer (MMCT) approach. Primary selection was carried out, and the cells were used to produce cloned bovine fetuses. Secondary selection was done on the regenerated fetal cell lines, which were then used to produce four healthy transchromosomic (Tc) calves. The HAC was retained at a high rate (78-100% of cells) in calves and the hIg loci underwent rearrangement and expressed diversified transcripts. Human immunoglobulin proteins were detected in the blood of newborn calves. The production of Tc calves is an important step in the development of a system for producing therapeutic hPABs.

Role of liver biopsy in the diagnosis of hepatic iron overload in the era of genetic testing

We studied hepatic iron overload (HIOL) patterns in 32 patients who underwent liver biopsies and testing for HFE mutations (C282Y, H63D). Iron-stained biopsy specimens were examined for patterns of iron deposits: hereditary hemochromatosis (HH) pattern or non-HH pattern. Visual iron grade based on amount of cellular and lobular iron was evaluated. We found the HH pattern in 17 biopsy specimens (53%) and the non-HH pattern in 6 specimens (19%). HH with superimposed non-HH was noted in 9 cases (28%). In 25 patients with HFE mutations, HH alone and combined with non-HH patterns was noted in 22 specimens (88%). Visual iron grade correlated approximately with the hepatic iron index. Heavy HIOL was noted in C282Y homozygotes and 1 patient with cirrhosis without either HFE mutation. Mild steatohepatitis was found in 21 specimens (66%); it was associated with the non-HH pattern in 80% (12/15) and the HH pattern in 62% (16/26) of cases. Liver biopsy can identify pattern and grade of HIOL and associated pathology for diagnosis and management of patients with abnormal iron studies and elevated liver function test results. Genetic tests for HFE mutations and liver biopsies are complementary in the workup of these patients.

Decisions about amniocentesis by advanced maternal age patients following maternal serum screening may not always correlate clinically with screening results: need for improvement in informed consent process

We evaluated the prenatal diagnosis utilization patterns of advanced maternal age (AMA) patients who underwent serum screening to assess how screening results correlated with their decisions regarding amniocentesis. A 6-year review (1994-1999) of laboratory records identified 2,456 AMA patients who underwent multiple-marker serum screening. The relationship between screening results and patients' decisions on whether or not to undergo amniocentesis was assessed. Among the 841 AMA patients with positive screens, more than half (52%) declined amniocentesis. Of the 1,615 patients with negative serum screening results, 208 (13%) opted for amniocentesis. We concluded that decisions by AMA patients regarding amniocentesis may not always correlate clinically with maternal serum screening results. Possible explanations, including how the state of informed consent may or may not contribute to these decisions, are discussed. It is suggested that understanding the reasons for these decisions may identify opportunities for improving service delivery to all pregnant patients considering prenatal testing. Use of a questionnaire is proposed as one mechanism for gaining a clearer understanding of the possible factors contributing to AMA patient decisions.

Tyrosine kinase activation in breast carcinoma with correlation to HER-2/neu gene amplification and receptor overexpression

The HER-2/neu oncogene encodes a transmembrane receptor with intrinsic tyrosine kinase activity. A pilot study was performed to investigate downstream effects of HER-2/neu (or related growth factor receptor) activation by identifying phosphorylated tyrosine. Fifty-four breast carcinomas were evaluated for HER-2/neu overexpression by the HercepTest (Dako, Carpinteria, CA) and the monoclonal CB11 antibody (Ventana, Tucson, AZ). Phosphotyrosine (an indication of tyrosine kinase activity) was detected by an antiphosphotyrosine mouse monoclonal antibody (Upstate Biotechnology, Lake Placid, NY). The gene amplification status was evaluated in 50 of the 54 cases by fluorescence in situ hybridization (FISH) using the Ventana gene probe. The HER-2/neu oncogene amplification was detected in 28% (14 of 50) of cases. Of the 14 cases showing oncogene amplification, tyrosine kinase activity was detected in 9 (64.2%) cases. There was moderate agreement between HER-2/neu gene amplification and tyrosine kinase activity (kappa = 0.43). Immunohistochemical staining of 3+ (with both HercepTest and CB11) showed better agreement with HER-2/neu oncogene amplification and increased tyrosine kinase activity than 2+ immunohistochemical staining. Overall, oncogene amplification and overexpression correlated with increased tyrosine kinase activity, supporting the mechanism of tyrosine kinase activation by HER-2/neu amplification and overexpression. However, 7 cases showing increased tyrosine kinase activity did not show gene amplification or 3+ receptor expression (by either HercepTest or CB11), raising the possibility of other growth factor receptors operating via the tyrosine kinase pathway. There was no apparent correlation between tyrosine kinase activity and hormone receptor status (estrogen or progesterone). Increased tyrosine kinase activity is more commonly associated with higher-grade tumors and thus may correlate with aggressive biologic behavior in breast carcinoma. The results of this pilot study suggest that a larger-scale investigation into downstream activation of tyrosine kinase and correlation to clinical outcome or response to Herceptin therapy may identify subsets of patients whose clinical response or outcome may be predicted by tyrosine kinase activation.

Cytogenetic studies of spontaneous miscarriages: a seven year study to compare significance of primary vs. secondary culture methods for assessment of fetal karyotype yield and maternal cell contamination

Primary in-situ culture (PIC) and secondary trypsinized culture (STC) are the two currently used methods for culturing chorionic villi in order to cytogenetically evaluate products of conception (POC) from spontaneous miscarriages. We compare these culture techniques in our laboratory over a period of seven years to evaluate fetal karyotype yield and maternal cell contamination. Data from a total of 2077 cases from 1992-1999 was entered into a data entry program created in Epi Info version 6. Analysis, using the chi square test of significance, was performed in the same program. Our data demonstrated a statistically significant excess of normal female karyotype detected by the STC method and a statistically significant excess of abnormal karyotypes detected by the PIC method. We attribute these findings to the greater risk of maternal cell contamination with the STC method. We conclude that the PIC method is more accurate in detecting the fetal karyotype and the STC method has a higher risk of maternal cell contamination. We suggest that the PIC method should be adopted as the method of choice when evaluating POC by culturing chorionic villi.

De novo translocation (8;12) and frontofacionasal dysplasia in a newborn boy

We describe a newborn boy one of triplets, whose karyotype was 46,XY, t(8;12)(q22;q21). Prenatal diagnosis of multiple craniofacial anomalies had been made. Following delivery, the patient was thought to exhibit findings consistent with a diagnosis of frontofacionasal dysostosis. We hypothesize that one of the break points of this translocation may involve a gene essential to craniofacial development.

Prenatal diagnosis and clinical features of an individual with tetrasomy 18p and trisomy 18q mosaicism

Prenatal diagnosis and clinical follow up of a patient with mosaicism for anomalies of chromosome 18 are reported. The fetus appeared on ultrasound to have multiple anomalies, including clubbed feet, abnormal hand positioning, edema of the scalp, cleft palate, and polyhydramnios. The karyotype on amniocytes was 47,XY,+i(18p). Postnatally, the peripheral blood karyotype was 46,XY,+i(18q), whereas the skin fibroblast karyotype was 47,XY,+i(18p). The infant had many features consistent with those previously described in cases of tetrasomy 18p and some that were consistent with trisomy 18q.

Reproduction in a patient with trisomy 8 mosaicism: case report and literature review

We describe a patient with trisomy 8 mosaicism followed through a sixth pregnancy and discuss issues in phenotypic and genotypic variability, the risk for neoplasia, and reproductive risks.

A five-year experience with fragile X testing. Setting laboratory standards of practice and a cost-effective protocol

During the years 1990-1994, our center tested 652 patients, with a broad range of referral indications, for fragile X syndrome using either cytogenetic analysis alone (Protocol 1) or more recently, a combination of DNA analysis and routine karyotyping (protocol 2). The overall positive rate for fragile X was 3.1% with an incidence of other chromosomal abnormalities (OCAs) of 3.2%. Breakdown of cases using each testing protocol along with percent positives is: [table: see text] Use of Protocol 2 yielded only definitive fragile X results, while more than half of the "positives" using Protocol 1 were equivocal. Historically this has been problematic for both the laboratory and physician since interpretation is often dependent on an equally equivocal clinical picture. Protocol 2 eliminates these diagnostic dilemmas without compromising detection of other chromosomal abnormalities, the incidence of which appears to be unaffected by testing method used. The overall incidence of OCA of 3.2% underscores the value of routine karyotyping in this referral group and likely reflects the phenotypic variability of fragile X and its clinical overlap with other chromosomal abnormalities. We believe that a fragile X testing protocol combining routine karyotyping with definitive molecular technology represents the most cost-effective diagnostic approach to this clinically challenging patient population.

Ring chromosomes in dermatofibrosarcoma protuberans are composed of interspersed sequences from chromosomes 17 and 22

Ring chromosomes are found in most dermatofibrosarcoma protuberans (DFSPs), and recent reports demonstrate that portions of the DFSP ring chromosomes derive from chromosome 17. In this study we characterized ring chromosomes in three DFSPs using a combined approach of karyotyping, chromosome painting, and comparative genomic hybridization. Chromosome painting demonstrated that the ring chromosomes in each DFSP were composed of discontinuous, interwoven sequences from chromosomes 17 and 22. Amplification of chromosomes 17 and 22 sequences was confirmed in each of these cases by comparative genomic hybridization, and over-representation of chromosomes 17 and 22 sequences was also demonstrated by comparative genomic hybridization in 1 of 2 cytogenetically unremarkable DFSPs. We conclude that amplification of chromosomes 17 and 22 sequences, in ring form, is a characteristic aberration in DFSP.

Translocation t(8;13)(p11;q11-12) in stem cell leukemia/lymphoma of T-cell and myeloid lineages

An unusual hematologic neoplasia has been described recently in which the predominant clinical features include T-cell lymphoma, myeloid hyperplasia, and eosinophilia. The multilineage involvement in this disorder suggests transformation of a primitive stem cell. Abnormal karyotypes have been described in three such cases, including one case with t(8;13)(p11.2;q12) and a second case with t(8;13)(p23;q14). We report translocation of chromosomes 8 and 13 in lymph node karyotypes from two patients with this syndrome. Fluorescence in situ hybridization confirmed an identical translocation, t(8;13)(p11;q11-12), in lymphoma cells from each patient. The translocation breakpoints are of particular interest because the FLT3 receptor tyrosine kinase gene has been mapped 13q12. FLT3 is expressed highly in hematopoietic progenitor cells and in myeloid and lymphoid acute leukemias.

Chromosome aberrations in desmoid tumors. Trisomy 8 may be a predictor of recurrence

Cytogenetic analyses of short-term cultures revealed clonal chromosome aberrations in 6 of 13 desmoid tumors. These aberrations included two consistent events, trisomy 8 (n = 4) and trisomy 20 (n = 3), which have not been reported previously in desmoid tumors. Because trisomy 8 was found in two recurrent desmoid tumors, we used fluorescent in situ hybridization (FISH) methodology to evaluate chromosome 8 in 25 paraffin-embedded and frozen desmoid specimens. The FISH studies demonstrated that both patients with cytogenetic trisomy 8 at the time of recurrence also had had trisomy 8 in primary tumors 4 years earlier. The proportion of trisomy 8 cells in these cases did not change substantially between original diagnosis and recurrence. The FISH studies also revealed trisomy 8 in one recurrent desmoid tumor which had been cytogenetically unremarkable and revealed trisomy 8 in one recurrent desmoid that had not been karyotyped. Four of six patients with trisomy 8 had been followed for more than 1 year, and the desmoid tumors in each of these 4 patients recurred. By contrast, recurrence was noted in only 2 of 17 patients whose desmoid tumors lacked trisomy 8. Our findings demonstrate that trisomy 8 and trisomy 20 are nonrandom aberrations in desmoid tumors. Trisomy 8 appears to be associated with an increased risk of recurrence.

Fluorescent in situ hybridization assessment of chromosome 7 copy number in uncultured lung and kidney cells

Trisomy 7 is common in cells cultured from nonneoplastic lung and kidney tissues, but the frequency of trisomy 7 in uncultured lung and kidney has not been determined. In this study, we used fluorescent in situ hybridization (FISH) to assess chromosome 7 copy number in uncultured interphase nuclei from lung and kidney specimens. All specimens had low level mosaicism for trisomy 7(1.5-5.25%), but control experiments indicated a potential wide margin of error in quantifying these events.

Clonal rearrangement of chromosome band 6p21 in the mesenchymal component of pulmonary chondroid hamartoma

Pulmonary chondroid hamartomas (PCH) are biphasic benign tumors that contain both mesenchymal and epithelial populations. In this report we describe two PCH in which clonal translocations at chromosome band 6p21 were demonstrated in mesenchymal cells. One of these had a unique translocation, t(6;14)(p21;q24), that was also found in one of two PCH karyotyped previously. The t(6;14) has not been described in other varieties of benign or malignant neoplasia. The 6p21 aberrations are of particular interest because break points in this chromosomal region appear to be characteristic of endometrial polyps. Endometrial polyps, like PCH, are biphasic benign tumors in which mesenchymal clonality has been demonstrated.