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.

Prospective analysis suggests susceptibility genes for deficiencies of IgA and several other immunoglobulins on the [HLA-B8, SC01, DR3] conserved extended haplotype.

The extended major histocompatibility complex (MHC) haplotype [HLA-B8, SC01, DR3] is increased in frequency among patients with immunoglobulin (Ig)A deficiency and common variable immunodeficiency. Because the genomic region from HLA-B to HLA-DR/DQ is virtually the same on all instances of the haplotype in the general population, we reasoned that all independent instances of [HLA-B8, SC01, DR3] carry MHC susceptibility genes for these disorders. To define immunoglobulin deficiencies determined by genes on this haplotype and their mode of expression and penetrance, serum immunoglobulin class and IgG subclass concentrations were determined prospectively in homozygotes and heterozygotes of this haplotype and in Caucasian controls. Prevalence of individual immunoglobulin deficiencies in persons with [HLA-B8, SC01, DR3] ranged from 13% to 37%, significantly higher than rates in non-carriers or general controls. We found significantly increased frequencies of IgA and IgG4 deficiency only in homozygotes (13.3% and 30%, respectively) compared with heterozygotes (1.7% and 3.4%) or non-carriers (1.6% each), suggesting recessive expression. In contrast, IgD and IgG3 deficiencies were significantly more common in both homozygotes (36.7% and 30%) and heterozygotes (20.3% and 17.5%) compared with controls (4.9% and 3.4%), suggesting dominant inheritance. These results indicate multiple distinct susceptibility genes, some recessive and others dominant, for deficiency of IgA, IgD, IgG3 or IgG4 (but not for IgE, IgG1, IgG2 or IgM) on [HLA-B8, SC01, DR3]. These observations may also help to explain the observed associations of [HLA-B8, SC01, DR3] with both IgA deficiency and common variable immunodeficiency and the common occurrence of IgG subclass deficiencies in some patients with IgA deficiency.

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.

Summary of validation studies from twenty-six forensic laboratories in the United States and Canada on the use of the AmpliType PM PCR amplification and typing kit.

A cooperative study was undertaken to collect and summarize the results of validation studies from forensic laboratories in the United States and Canada on the use of the AmpliType PM PCR amplification and typing kit for genetic typing of forensic biological evidence. This report compiles data from 26 laboratories on: 1) reproducibility studies on DNA extracted from various samples, 2) genetic typing of DNA extracted from a variety of biological samples on various substrates, 3) the effects of exogenous chemicals, materials, and environmental factors on test results, 4) sensitivity studies to determine the least detectable amount of extracted genomic DNA that can be reliably typed, 5) analysis of mixtures containing two sources of genomic DNA, 6) cross-hybridization with DNA extracted from various nonhuman species, and 7) evaluation of assay performance on parallel studies with other genetic typing systems on proficiency test panels, mock cases, and adjudicated/nonprobative casework. Equivalent results were obtained by each laboratory that supplied data, demonstrating the reliability and consistency of the test. Overall, it can be concluded from this study that the AmpliType PM PCR amplification and typing kit meets the guidelines of the Technical Working Group on DNA Analysis Methods (TWGDAM) and there is general scientific acceptability of this kit for forensic DNA testing.

Nonrandom inactivation of the X chromosome in early lineage hematopoietic cells in carriers of Wiskott-Aldrich syndrome.

The Wiskott-Aldrich syndrome (WAS) is an X-linked (Xp11.22) recessive immunodeficiency syndrome characterized by susceptibility to opportunistic and pyogenic infections, thrombocytopenia, and eczema. Previous studies of obligate carriers of WAS documented that nonrandom inactivation of the X chromosome carrying the defective gene is observed in all peripheral blood cells. The existence of both abnormal platelets and lymphocytes is consistent with a defect that affects early hematopoietic precursors. We isolated CD34+ hematopoietic progenitor cells collected from obligate carriers of WAS by apheresis and used polymerase chain reaction analysis of a polymorphic variable number of repeats (VNTR) within the X-linked androgen receptor to document nonrandom inactivation. These data show that nonrandom inactivation of the X-chromosome in WAS-obligate carriers occurs early during hematopoietic differentiation.

Major histocompatibility complex class II alleles and haplotypes and blood groups of four Amerindian tribes of northern Colombia.

MHC class II alleles and haplotypes were determined from unrelated individuals and families of the Arhuaco (n = 107), Kogi (n = 42), Arsario (n = 18), and Wayú (n = 88) tribes located in the northern part of Colombia. Class II DRB, DQA1, and DQB1 alleles were determined by PCR-SSO and PCR-RFLP based methods. Four haplotypes, [DRB1*0407, DRB4*0101, DQA1*03, DQB1*0302]; [DRB1*0403, DRB4*0101, DQA1*03, DQB1*0302]; [DRB1*1402/1406, DRB3*0101, DQA1*0501, DQB1*0301]; and [DRB1*0802, DQA1*0401, DQB1*0402], were observed among these four tribes. In addition to these haplotypes, the Wayú Indians showed a frequency of 21.3% for the [DRB1*1602, DRB5*02, DQA1*0501, DQB1*0301] haplotype, 13.1% for the [DRB1*0411, DRB4*0101, DQA1*03, DQB1*0302] haplotype, and 8.1% for the [DRB1*0411, DRB4*0101, DQA1*03, DQB1*0402] haplotype. Red cell antigen typing was used to calculate genetic admixture. The Kogi and Arsario showed no genetic admixture while the Arhuaco tribe showed admixture with genes of African origin and the Wayú showed admixture with Caucasians as well as genes of African origin. These findings were confirmed by the MHC class II allele and haplotype data obtained, as alleles and haplotypes of Caucasian and African origin were detected in the Wayú and Arhuaco and not in the Kogi or Arsario. These studies will be important in disease association and transplantation studies for Amerindian and colombian populations and for correlating genetic traits with the anthropologic and linguistic data available in order to better understand the Amerindian populations.

Acquired C1 inhibitor deficiency as a result of an autoantibody to the reactive center region of C1 inhibitor.

An autoantibody that we hypothesize to react with the reactive center of the plasma serine proteinase inhibitor, C1 inhibitor (C1INH), has been found in a patient with acquired C1INH deficiency. The Ab blocks the ability of C1INH to inhibit the hydrolysis of N-carbobenzyloxy-L-lysine thiobenzylester by purified C1s. A cryoprecipitate from the patient's plasma as well as the Ig fraction were able to block C1INH inhibition of C1s. The immunoaffinity purified Ab to C1INH from the patient's plasma Ig fraction neutralizes the inhibitory activity of C1INH in a dose-dependent manner and blocks the ability of normal C1INH to form a complex with C1s. The neutralizing activity of the purified Ab is reversed by a synthetic peptide that corresponds to the amino acid sequence in the P1 to P15 positions of the reactive center of C1INH but not by a 34-amino-acid trypsin peptide or 37-amino-acid elastase peptide derived from the C-terminus of C1INH. Western blot analysis indicated that the Ab is an oligoclonal Ig with kappa light chains.

Genetic typing of the DQA1*4 alleles by restriction enzyme digestion of the PCR product obtained with the DQ Alpha Amplitype kit.

The three DQ Alpha 4 alleles, 4.1 (0501), 4.2 (0401), and 4.3 (0601) cannot be distinguished with the reverse dot blot DQ Alpha Amplitype Kit. A previous report (Yunis, I. et al., Tissue Antigens, Vol. 39, 1992, pp. 182-186) indicated that the typing of these three alleles can be accomplished by endonuclease digestion of the PCR product that is produced following amplification with the DQ Alpha primers with Fok I and Rsa I. We report here the use of this method to type the DQA1*0401, 0501 and 0601 alleles in the PCR product obtained with the DQ Alpha-Amplitype Kit. We have analyzed the PCR product obtained in over 200 forensic samples. We have found that in all of these cases, it is possible to assign a type to those samples that type as DQ Alpha 4 with the Amplitype Kit. Furthermore, we have found the technique to be useful in some cases where it has not been previously possible to distinguish individuals or samples that have the DQ Alpha 4 allele and type identically with respect to all other DQ Alpha alleles.

Cellular recognition and HLA restriction of a midsequence HBsAg peptide in hepatitis B vaccinated individuals.

Vaccination with native HBsAg results in both a humoral and a cellular immune response in humans. In individuals who responded to vaccination, the HBsAg (S region) specific response, as measured by cell proliferation, diminished significantly after 12 weeks, a time when the antibody response was still vigorous. Reduced and nonreduced HBsAg were equivalent in eliciting lymphocyte proliferation. Anti-MHC class II monoclonal antibodies were used in blocking studies to demonstrate that anti-HLA-DR but not anti-HLA-DQ or anti-HLA-DP inhibited specific lymphocyte proliferation to HBsAg. Both the monomer (reduced) and dimer (nonreduced) forms of an immunodominant midsequence HBsAg peptide (amino acid residues 139-146) produced lymphocyte proliferation roughly comparable to that induced by whole HBsAg in 6 of 7 responders immunized with whole HBsAg and the peptide-induced proliferation was blocked by anti-HLA-DR but not by anti-HLA-DP antibodies. These results suggest that HBsAg p 139-146 is a major immunodominant peptide of HBsAg and is restricted by HLA-DR.

HLA-DQA1, DQB1 and DPB1 alleles on HLA-DQ2- and DQ9-carrying extended haplotypes.

DQA1, DQB1 and DPB1 alleles were investigated in a large panel of samples carrying HLA-DQ2- and HLA-DQ9-bearing extended haplotypes. Every instance of the [HLA-B8, SCO1, DR3, DQ2a] and [HLA-B18, F1C30, DR3, DQ2b] extended haplotypes carried the DQA1*0501 allele, while every instance of [HLA-B44, FC31, DR7, DQ2c], [HLA-B47, FC91,0, DR7, DQ2c] and [HLA-B57, SC61, DR7, DQ2d] carried the DQA1*0201 allele. All HLA-DR3, DQ2 and HLA-DR7, DQ2 extended haplotypes carried the DQB1*0201 allele. Every example of [HLA-B57, SC61, DR7, DQ9] carried the DQB1*0303 allele. Several associations between the DPB1 alleles and some HLA-DQ2- and DQ9-carrying extended haplotypes were identified. HLA-DPw2-encoding alleles, DPB1*0202 (50%, p < 0.001) and 0201 (30%), were found on the [HLA-B18, F1C30, DR3, DQ2b] extended haplotype. Every instance of the [HLA-B57, SC61, DR7, DQ9] extended haplotype carried the DPB1*0401 allele. Also, we have confirmed the associations of the DPB1*0101 and DPB1*0401 alleles with the [HLA-B8, SC01, DR3, DQ2a] extended haplotype. The analysis of homozygous typing cells carrying the [HLA-B44, FC31, DR7, DQ2c] extended haplotype showed that the DPB1*0401 and 0201 alleles were present at similar frequencies (37.5%), while the DPB1*1101 allele was found in only 25% of these haplotypes analyzed. Our results suggest that the constancy of the DNA of the HLA-B, DR, DQ regions may extend to the DP region and that the extent of such fixity varies, perhaps as the result of ethnic variability of the population studied.

Synthesis of the third component of complement (C3) by lectin-activated and HTLV-infected human T-cells.

The third component of complement (C3) plays key roles in complement activation of both the classical and alternative pathways. The liver is the major site of C3 synthesis; monocytes, B-lymphocytes and leukemic cell lines of the myeloid lineage also synthesize C3. Here we report that the C3 gene is inactive in fresh T-cells, but active in T-cells treated with the lectin phytohemagglutinin (PHA). Northern blot hybridization studies show that PHA-activated T-cells and all the T-cell lines tested express the 5.3 kb RNA transcript reported for C3 in HepG2, a hepatoma cell line, and monocytes. We used radioimmune precipitation followed by polyacrylamide gel electrophoresis to show that PHA-stimulated T-cells and T-cell lines, which are not infected with the human T-lymphotropic virus (HTLV), synthesize and release C3 proteins with molecular masses of 185, 115 and 80 kD; HTLV-infected T-cell lines release C3 proteins of 170, 115 and 70 kD. In contrast, monocytes produced C3 proteins of 115 and 70 kD similar to the serum form of this protein. The role of T-lymphocyte C3 and the implications of HTLV-infection are discussed.

Factor J: isolation and characterization of a new polypeptide inhibitor of complement C1.

An Mr 20,000 protein inhibitor of C1, the first component of complement, has been purified from human urine and characterized. This inhibitor, tentatively designated factor J, is apparently distinct from known complement inhibitors. During purification on QAE-Sephadex, Mono Q, and heparin-Sepharose, factor J was detected by its ability to inhibit the complement-mediated lysis of sheep erythrocytes bearing antibody, C1, and activated C4 (EAC14). The purity of factor J was documented by the concordant elution from a hydroxylapatite column of functional activity and the UV absorbance as measured at three different wavelengths (220, 254, and 280 nm). The relative Mr of 20,000 was determined by sodium dodecyl sulfate-slab gel electrophoresis of radioiodinated protein. Amino acid analysis indicated a high cysteine content and allowed calculations of a specific activity of 7 functional units/pmol. The target of factor J inhibitory activity on the lysis of EAC14 was localized to C1 by the following criteria: factor J inhibited C1 in a C1 transfer assay, but had no effect on C42 activity or decay, and had no effect on the efficiency of isolated C2 or C3-C9 as provided in serum-EDTA. Factor J inhibition was rapid and not significantly influenced by temperature. In a second functional assay, factor J inhibited the association of the tetrameric complex C1r2s2 with 125I-C1q, and the results, when analyzed graphically by a reciprocal plot, were consistent with noncompetitive inhibition (Ki = 529-760 pM range). Functional and/or antigenic data indicated that factor J is distinct from the other known inhibitors of C1, namely the C1 inhibitor and the C1q inhibitor. Antihuman serum precipitated radioiodinated factor J, indicating that an antigen identical or cross-reacting with factor J exists in serum. In summary, factor J is a newly described potent inhibitor of C1 function.

Amelioration of immune complex-mediated glomerulonephritis by synthetic protease inhibitors.

Proteases are involved in the pathogenesis of inflammatory diseases by participating in the activation of mediator systems and by producing proteolytic tissue injury. Homeostatic control of inflammation is accomplished in part by physiologic protease inhibitors. The authors investigated the effectiveness of a number of synthetic protease inhibitors in ameliorating the glomerular injury induced by immune complex-mediated glomerulonephritis in mice. Two amidine-type protease inhibitors, bis (5-amidino-2-benzimidazolyl)methane and 1,2-bis (5-amidino-2-benzimidazolyl)ethane, had the greatest effects. They caused a marked reduction in glomerular necrosis (P less than 0.001) but did not affect the amount or site of immune complex localization or leukocyte influx. The inhibition constants of the protease inhibitors against nine purified physiologic proteases were determined. These results were discussed in relation to the effectiveness of the protease inhibitors in reducing glomerular injury. This investigation indicates that the administration of synthetic protease inhibitors can have a beneficial effect on immune-mediated inflammatory injury.

Transcriptional regulation of genes encoding the acute-phase proteins CRP, SAA, and C3.

Inflammation or acute tissue injury results in a programmed change in the concentration of several plasma proteins. Among these proteins, two--C-reactive protein (CRP) and serum amyloid A protein (SAA)--increase up to 1000-fold after an acute-phase stimulus in humans and rabbits. To determine the mechanism for regulation of acute-phase gene expression, we examined changes in the rates of transcription and specific hepatic mRNA content for rabbit CRP, SAA, and some complement protein mRNA during an acute-phase response. Induction of a sterile inflammatory reaction with intramuscular injection of turpentine resulted in an increase in the hepatocellular content of CRP, SAA, C3, and factor B mRNA and the transcription of CRP, SAA, and C3 genes. These data suggest that the increase in CRP, SAA, and C3 serum concentrations observed during an acute-phase reaction is due to an increase in biosynthesis and is, at least in part, under transcriptional control.

Interactions of plasma kallikrein and C1-s with normal and dysfunctional C1(-)-inhibitor proteins from patients with hereditary angioneurotic edema: analytic gel studies.

Purified preparations of normal C1(-)-inhibitor (C1(-)-INH) formed high mol wt complexes with plasma kallikrein that were stable during sodium dodecyl sulfate (SDS)-gel electrophoresis, but most of the dysfunctional C1(-)-INH proteins isolated from plasma of patients with type II hereditary angioneurotic edema (HANE) did not. Two of eight dysfunctional C1(-)-INH proteins were cleaved to lower mol wt forms that were not seen following the reaction of normal C1(-)-INH with equimolar amounts, or less, of plasma kallikrein. Only the higher mol wt component of normal C1(-)-INH (106,000 mol wt) appeared to form a stable complex with the plasma kallikrein, whereas both the 106,000 and 96,000 mol wt forms made stable complexes with C1-s. When a preparation of normal C1(-)-INH containing a homogeneous single band of C1(-)-INH was exposed to C1-s or kallikrein, a "doublet" form evolved in which the heaviest band was in the original position of native C1(-)-INH; C1-s cleavage provided a second band of 96,000; and cleavage by kallikrein, a second band of 94,000 mol wt. We conclude that dysfunctional C1(-)-INH proteins from plasma of persons with type II hereditary angioneurotic edema have impaired interactions with plasma kallikrein and are heterogeneous with respect to these interactions. Moreover, the requirements for the formation of stable complexes between normal C1(-)-INH and plasma kallikrein differed from those for stable complex formation with C1-s. The doublet form of C1(-)-INH, which purified preparations frequently demonstrate, may be due to prior cleavage by C1-s or kallikrein.