Interpretation of complex forensic DNA mixtures.

Forensic evidentiary samples routinely contain DNA from multiple contributors. The interpretation of these mixtures can be a challenging task for the DNA scientist. Several approaches are discussed (no calculation- qualitative statement; probability of exclusion; likelihood ratio estimates; presumptive genotype assignment based on peak heights), which have been employed to assess the significance of an inclusion/match when DNA mixtures have been detected in casework samples. These statistical approaches are discussed in light of technical challenges that can arise when evaluating evidentiary samples.

Fluorescence in situ hybridization (FISH) for rapid detection of aneuploidy: experience in 911 prenatal cases.

Fluorescence in situ hybridization (FISH) was performed with probes specific for chromosomes 13, 18, 21, X and Y on 911 of 11123 (8.2%) amniotic fluid samples submitted to the present authors' laboratory for cytogenetic analysis over an 8-year period. Altogether 3516 hybridizations were performed with an interpretable FISH result on all chromosomes requested in 884/911 (97%) of cases. An uninformative FISH result occurred in 44 hybridizations among 27 cases (3%). Of a total of 89 karyotypically proven cases with aneuploidy that might have been detected by FISH, the overall detection rate was 84%. An inconclusive or incomplete FISH result occurred in 9/89 (10%) of these proven aneuploid cases. In the remaining 80 informative proven aneuploid cases, correct detection of aneuploidy was accomplished in 75/80 (94%) of samples. A false-negative result occurred in the remaining 5/80 (6%) of such informative cases. Eighteen cases had karyotypically proven abnormalities that could not have been detected by the targeted FISH. Aside from these 18 cases, FISH allowed correct detection of normal disomy in 785/804 (98%) of such cases. An incomplete FISH result occurred in 18 normal disomic cases. There was a single possible 'false-positive' FISH result for chromosome 21. Interphase FISH analysis of uncultured amniotic fluid cells has been shown to be a useful laboratory tool for rapid fetal aneuploidy screening during pregnancy. As with all clinical laboratory diagnostic tests, incomplete or inconclusive results (or even interpretive errors) occur in a small percentage of cases. Nevertheless, FISH results accompanied by other data and by appropriate counseling provide clinicians and patients with valuable information for clinical decision-making surrounding family planning and pregnancy management.

Overview of human identity testing and forensic genetics.

This unit discusses the development of the field of forensic genetics, touching on the quality control and legal issues that are central to this area. It closes with a discussion of some caveats for interpreting forensic DNA results.

Collecting and handling samples for parentage and forensics DNA-based genetic testing.

The unit covers Variable Numbers of Tandem Repeats (VNTR) based paternity analysis as well as the newer methods relying on PCR to analyze sequence specific polymorphisms and microsatellite regions. The discussion of data analysis and probability calculations has been expanded to address a number of special circumstances, such as the lack of sample from an alleged father, motherless cases, and more.

Isolation of DNA from forensic evidence.

This unit covers the many and varied methods for extracting DNA from such diverse specimens as blood, tissue, stamps and envelopes, and cigarette butts, among others. Modifications to the methods that allow the DNA to be used for either PCR or Southern blotbased analyses are also included.

RFLP analysis of forensic DNA samples with single-locus VNTR genetic markers.

This unit covers the many and varied methods for extracting DNA from such diverse specimens as blood, tissue, stamps and envelopes, and cigarette butts, among others. Modifications to the methods that allow the DNA to be used for either PCR or Southern blotbased analyses are also included.

Manual methods for PCR-based forensic DNA analysis.

This unit provides validated PCR-based methods to test for sequence polymorphisms and length polymorphisms. It includes a description of the reverse dot blot method for detecting sequence polymorphisms. The forensic PCR systems used to detect length polymorphisms are based on detection of different-sized PCR products following electrophoresis in either native or denaturing polyacrylamide gels. The unit offers a description of the amplification and detection of the variable number of tandem repeat (VNTR) length polymorphism at the D1S80 locus. It also describes the multiplex amplification of three separate autosomal short tandem repeats (STRs) and the X- and Y-linked amelogenin alleles. These PCR products are electrophoresed on a denaturing polyacrylamide gel. Support protocols for creating permanent records of silver-stained gels, checking the quality of reagents, and interpreting PCR-based tests are provided.

Detection of mosaicism in amniotic fluid cultures: a CYTO2000 collaborative study.

PURPOSE: To evaluate the assumptions on which the American College of Medical Genetics (ACMG) Standards and Guidelines for detecting mosaicism in amniotic fluid cultures are based. METHODS: Data from 653 cases of amniotic fluid mosaicism were collected from 26 laboratories. A chi-square goodness-of-fit test was used to compare the observed number of mosaic cases with the expected number based on binomial distribution theory. RESULTS: Comparison of observed data from the in situ colony cases with the expected distribution of cases detected based on the binomial distribution did not reveal a significant difference (P = 0.525). CONCLUSIONS: The empirical data fit the binomial distribution. Therefore, binomial theory can be used as an initial discussion point for determining whether ACMG Standards and Guidelines are adequate for detecting mosaicism.

Twins, placentas, and genetics: acardiac twinning in a dichorionic, diamniotic, monozygotic twin gestation.

We describe a human acardiac twin with associated vascular anastomoses in a dichorionic diamniotic fused twin placenta. A 22-year-old woman delivered a healthy 3,554 g male infant and a fused diamniotic dichorionic twin placenta with a 230 g umbilical cord-attached, skin-covered, ovoid mass, consistent with acardiac amorphus. By gross and histological examination, the placental dividing membranes comprised four leaves, one amnion from each placenta, and two centrally fused chorions, diagnostic of dichorionicity. Placental barium injection of the normal twin's umbilical vein showed an anastomosis with the acardiac twin which traversed the dividing membranes, then supplied major vessels of the acardiac mass via its 5.5 cm umbilical cord. DNA-typing studies of the normal twin's placenta and of the acardiac twin's tissues revealed identical alleles at 11 distinct genetic polymorphic loci, consistent with monozygosity. Our findings demonstrate that vascular anastomoses can occur in dichorionic twin placentas, and that human acardiac twinning is not, as heretofore believed, restricted to monochorionic placentas.

An ancient conserved gene expressed in the human inner ear: identification, expression analysis, and chromosomal mapping of human and mouse antiquitin (ATQ1).

We constructed and screened a human fetal cochlear cDNA library to identify genes involved in hearing and deafness. From this library we isolated a cDNA corresponding to the highly conserved ancient gene antiquitin (ATQ1). The plant homolog of ATQ1 is thought to be involved in regulating turgor pressure, a function that also would be essential for cells of the mammalian cochlea. Northern blots of 13 human fetal tissues show antiquitin to be highly expressed in cochlea, ovary, eye, heart, and kidney. Using RT-PCR of rat cochlear hair cell-specific cDNA libraries, we detect antiquitin expression in outer hair cells, but not in inner or vestibular type 1 hair cells, suggesting that antiquitin is not expressed ubiquitously in the cochlea. Human ATQ1 was mapped to human chromosome region 5q31 using fluorescence in situ hybridization, and mouse ATQ1 was mapped to mouse chromosome 18 by single-strand conformation polymorphism mapping of interspecific backcross progeny DNAs. Four human antiquitin-like sequences, possibly pseudogenes, were also identified and mapped.

Mapping and characterization of a novel cochlear gene in human and in mouse: a positional candidate gene for a deafness disorder, DFNA9.

Previously we identified a partial human cDNA for a novel cochlear transcript, hCoch-5B2 (HGMW-approved symbol D14S564E), using subtractive hybridization techniques. Herein we report isolation and characterization of both human and mouse (D12H14S564E) cDNAs for Coch-5B2. Full-length Coch5B2 deduced amino acid sequences reveal a very high degree of conservation in the coding region (89% nucleotide and 94% amino acid identity and a potential signal peptide and two regions of extensive homology to the collagen-binding type A domains of von Willebrand factor, also present in other secreted proteins, including extracellular matrix components. High levels of hCoch-5B2 expression are seen only in human fetal inner ear structures, cochlea, and vestibule, among a large panel of human fetal and adult tissues. Coch-5B2 expression in the mouse is more widespread than in the human, with message detected in mouse adult spleen, cerebrum, cerebellum/medulla, and thymus. In both species very low level expression is detected in total eye. More specifically, mouse retina shows a higher level of mCoch-5B2 message than sclera and choroid. We have mapped hCoch-5B2 to human 14q11.2-q13 by somatic cell hybrid analysis and FISH and, more precisely, using radiation hybrids to a region of markers linked to DFNA9, a nonsyndromic autosomal dominant sensorineural hearing loss with vestibular defects. Furthermore, we detect hCoch-5B2 on three overlapping YACs, two of which also contain one of the markers linked to DFNA9. mCoch-5B2 was genetically mapped in the mouse to chromosome 12, in a region of homologous synteny with human 14q11.2-q13, which contains the asp1 (audiogenic seizure prone) locus in the mouse.

Epidemiology of osteochondrodysplasias: changing trends due to advances in prenatal diagnosis.

The osteochondrodysplasias (skeletal dysplasias) are a heterogeneous group of disorders characterized by abnormalities in cartilage and bone growth and development. Some of these disorders are detectable during the second trimester by sonographic techniques. We ascertained cases of osteochondrodysplasias in elective pregnancy terminations, stillborn infants older than 20 gestational weeks, and liveborn infants diagnosed by the fifth day of life as part of an ongoing active malformation surveillance program. Forty-nine cases of osteochondrodysplasias were identified among approximately 126,000 deliveries at Brigham and Women's Hospital (BWH) during a 15-year period (Feb. 16, 1972-Feb. 15, 1975; Jan. 1, 1979-Dec. 31, 1990). When cases delivered to women who had planned to deliver at another hospital but were transferred for high-risk care (transfers) were excluded, the prevalence rate was 2.14 cases per 10,000 deliveries. During the early period (1972-1975) no cases were suspected prenatally, while during the 1988-1990 period, 80% of all cases and 57% of cases delivered to women who had always planned to deliver at BWH (non-transfers) were suspected by ultrasonography. Birth status changed through our period of surveillance. In the final 3-year period (1988-1990), 40% of all cases and 29% of non-transfers with osteochondrodysplasias were pregnancy terminations, compared to none during the 1972-1975 period. The increasing frequency of pregnancy terminations complicated the diagnosis of these conditions. Despite extensive evaluation, a definitive diagnosis was not possible in 8 of 49 cases (16%). Biochemical and molecular genetic methods of diagnosis will continue to become more important if the current trend of wide utilization of prenatal sonography and termination of affected pregnancies continues.

Massive chronic intervillositis associated with recurrent abortions.

Massive chronic intervillositis (MCI) is an unusual placental lesion associated with poor fetal growth and adverse pregnancy outcome; it has not previously been associated with spontaneous abortion or recurrent pregnancy loss. This article reports a patient who had 10 spontaneous abortions with repetitious massive chronic intervillositis documented in four of five gestations spanning all three trimesters. Characteristic placental histology induced massive infiltration of the maternal intervillous space by chronic inflammatory cells and fibrin, without associated chronic villitis; the cellular infiltrate was composed predominantly of LCA and CD68 immunoreactive cells with scattered CD45RO positivity, consistent with a monocyte/macrophage population with occasional T lymphocytes. Elevated maternal serum alpha-fetoprotein was documented in two pregnancies. These findings support the concept that this unusual placental lesion may have an immunologic basis, and suggest that MCI may be a histopathologically recognizable cause of recurrent spontaneous abortion.

GNAZ in human fetal cochlea: expression, localization, and potential role in inner ear function.

Dissociation of an activated alpha-subunit from the beta-gamma complex directly regulates secondary messenger proteins. To address the potential role of G proteins expressed in human fetal cochlea, degenerate oligonucleotide primers corresponding to the 3'-end of the conserved region of alpha-subunits were used for polymerase chain reaction amplification of reverse-transcribed total human fetal cochlear mRNAs; GNAZ and GNAQ were isolated. These two G proteins are unique among the G-protein family because they lack a typical pertussis modification site. GNAZ is expressed in high levels in neural tissue while GNAQ is ubiquitously expressed. We characterized GNAZ expression using Northern blots, tissue in-situ hybridization and immunohistochemistry techniques to elucidate the potential role of this protein in inner ear function. Our data suggest that GNAZ may play a role in maintaining the ionic balance of perilymphatic and endolymphatic cochlear fluids.

Fetoplacental histology as a predictor of karyotype: a controlled study of spontaneous first trimester abortions.

It has been suggested that inferences about fetal karyotype can be made from examination of placental and decidual histology in early, spontaneous abortions (SABs). We assessed the reproducibility and predictive value of histologic features in 75 karyotyped, first trimester SABs; 32% (24 of 75) had normal male karyotypes (46,XY) and 68% (51 of 75) were cytogenetically abnormal (29 trisomy, 12 triploidy, eight monosomy X, and two tetraploidy). Three pathologists independently assessed 17 fetal, placental, and decidual histological findings and made predictions about the karyotype (normal, abnormal, or uncertain). Good to excellent interobserver and intraobserver reproducibility (kappa > 0.58) was achieved for the identification of five histological features: villous cavitation, anucleate fetal erythrocytes, amnion, umbilical cord, and fetal tissue. When histology and karyotype were compared using Fisher's exact test, no histological feature was associated with "any abnormal karyotype," two features (anucleate, fetal erythrocytes and umbilical cord) were associated with a normal karyotype, two features (villous dysmorphism and cisterns) were associated with triploidy, and four features (villous hydrops, no umbilical cord, no fetal tissue, and no anucleate erythrocytes) were associated with trisomy. Despite these significant histological-cytogenetic associations, the positive predictive values of each of these histological features with their corresponding karyotypes were low, ranging from 0.41 to 0.73 (mean, 0.53). Our data suggest that certain histological features in first trimester SABs are associated with the SAB's karyotype and are reproducible; however, such histological features did not perform as well as diagnostic tests for predicting the likelihood of normal versus abnormal karyotype.

Expression of the Kallmann syndrome gene in human fetal brain and in the manipulated chick embryo.

Kallmann syndrome is an inherited disorder characterized by an abnormality in olfactory system development. The gene for the X-linked form of this disorder (KAL) maps to Xp22.3 and encodes a protein sharing homologies with molecules involved in neuronal migration and axonal pathfinding. Here we report the expression pattern of the KAL gene in various parts of the human fetal brain. We found KAL transcripts in granule cells of the olfactory bulb and the cerebellum, in the dorsomedial thalamus and in the developing cerebral cortex. To determine whether or not signals from the olfactory nerve are required for KAL expression in the olfactory bulb, we analyzed chick embryos in which the olfactory placode was surgically removed. Those embryos lacking an olfactory nerve had a histologically abnormal bulb which nevertheless expressed the KAL gene at high levels. These findings indicate that, while the development of the proper cytoarchitecture of the olfactory bulb requires the innervation by olfactory axons, the expression of KAL is independent of such developmental processes.

Isolation of novel and known genes from a human fetal cochlear cDNA library using subtractive hybridization and differential screening.

We used a combination of subtractive hybridization and differential screening strategies to identify genes that may function normally in hearing and, when mutated, result in deafness. A human fetal cochlear (membranous labyrinth) cDNA library was subtracted against total human fetal brain RNAs by an avidin-biotin-based procedure to enrich for cochlear transcripts. Subtracted cochlear clones were differentially screened with 32P-labeled total cochlear and total brain cDNA probes. Sequence analysis of clones that hybridized more intensely with cochlear than with brain cDNA probes revealed some previously characterized genes, including mitochondrial sequences, collagen type I alpha-2 (COL1A2), collagen type II alpha-1 (COL2A1), collagen type III alpha-1 (COL3A1), spermidine/spermine N1-acetyltransferase (SAT), osteonectin (SPARC), and peripheral myelin protein 22 (PMP22). Also identified were clones that are potential novel cochlear genes. Northern blots of cochlear and brain RNAs probed with COL1A2, COL2A1, COL3A1, SAT, SPARC, PMP22, and a novel sequence, designated Coch-5B2, confirm results of the subtractive procedure by showing preferential cochlear expression. A number of these genes serve structural or regulatory functions in extracellular matrix or neural conduction; defects in some of these genes are associated with disorders involving hearing loss. Partial sequence analysis of Coch-5B2 reveals a von Willebrand factor type A-like domain in this cDNA. To assess the cochlear specificity of Coch-5B2, a Northern blot panel of 14 human fetal tissue RNAs was probed with Coch-5B2, showing differential expression of this novel gene in the cochlea.

Prenatal sonography in trisomy 9.

Two cases of trisomy 9 are presented with the description of the prenatal sonographic findings prompting prenatal cytogenetics evaluation. The characteristic sonographic abnormalities included structural heart defects; limb, renal, and facial anomalies; and intrauterine growth retardation. The clinical course and cytogenetic and autopsy finding are described.

Etiologic complexities of diaphragmatic defects: right diaphragmatic hernia, pulmonary hypoplasia/agenesis, and hydrocephalus in sibs.

Here we review the complexities of diaphragmatic defects and describe sibs with small, right diaphragmatic defects with pulmonary hypoplasia/agenesis and hydrocephalus. Despite a poor initial prognosis, the propositus has progressed remarkably well. Antenatal sonographic study detected hydrocephalus but not the diaphragmatic defect in the sib of the propositus. Because diaphragmatic defects are most commonly found in association with other anomalies and may occur in association with chromosome anomalies careful workup of all affected infants is crucial for accurate genetic counseling.