Search PubMed⌕ Search

Biomedical subjects

B Budowle

Publications and source records attributed to B Budowle.

At least 181 records · Page 10Linked to original sources
PubMed1992

Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications.

Restriction fragment length polymorphisms (RFLP) analysis using the Southern blot technique can be used to recognize copy number variation of variable number of tandem repeats (VNTR) of conserved core sequences at several regions of the human genome. This new class of polymorphisms reveals a high degree of genetic variation, useful for individual identification purposes. Criticisms against forensic applications of such DNA typing data include the limitation of employing Hardy-Weinberg expectation of genotype frequencies, since several surveys indicate apparent deficiency of heterozygosity (or excess homozygosity) in comparison with Hardy-Weinberg expectations. This research postulates an alternative explanation of deficiency of apparent heterozygosity which is caused by the inability to detect extremely small-sized alleles (called 'non-detectable' alleles) due to the sensitivity of Southern gel electrophoresis. We show that the presence of 'non-detectable' alleles can produce pseudo-homozygosity and their frequencies can be predicted from the observed proportional heterozygote deficiency. Furthermore, in the covert presence of such 'non-detectable' alleles, we show that the gene-count method provides over-estimates of allele frequencies in the sample population, and hence the Hardy-Weinberg predictions of genotype frequencies avoid wrongful bias against suspects in forensic applications of DNA typing data. Applications of this theory to population data on six VNTR loci in US Caucasians and US Blacks suggest that the presence of 'non-detectable' alleles could be the major cause of apparent heterozygote deficiency, and the current approaches of predicting the population frequency of specific DNA phenotypes are practically free of the possible wrongful bias in courtroom applications of DNA typing data.

Alleles↗
PubMed1992

PCR amplification of alleles at the DIS80 locus: comparison of a Finnish and a North American Caucasian population sample, and forensic casework evaluation.

Allele and genotype frequencies for the highly polymorphic D1S80 locus were determined in a Finnish population sample by using PCR followed by high-resolution PAGE and silver staining, a procedure called the amplified-fragment-length polymorphism (Amp-FLP) technique. In 140 unrelated Finnish individuals 15 alleles and 43 phenotypes were observed. The D1S80 locus demonstrated a heterozygosity of .77, and the power of discrimination was .92 in this sample representing a genetically isolated Finnish population. The distribution of observed genotypes conformed to Hardy-Weinberg expectations. In 36 mother-child pairs Mendelian inheritance for the alleles at the D1S80 locus could be demonstrated in all cases, and no mutations were observed. The usefulness of the D1S80 locus for forensic casework was assessed by using Amp-FLP analysis of the D1S80 locus in 36 forensic cases including 18 rapes, 14 homicides, and 4 other violent crimes. In most cases valuable information was obtained using the Amp-FLP technique, and in no case was there indication of either false-positive or false-negative results.

Alleles↗
PubMed1992

Effect of storage conditions on restriction fragment length polymorphism (RFLP) analysis of deoxyribonucleic acid (DNA) bound to positively charged nylon membranes.

The ability to generate an autoradiogram from deoxyribonucleic acid (DNA) immobilized on a positively charged nylon membrane could be compromised by the storage conditions of the membrane. HaeIII-digested human DNA was size fractionated and transferred to two types of positively charged nylon membranes. The membranes were stored at -20 degrees C, 4 degrees C, and ambient temperature and humidity for times ranging from 1 day to 13 weeks, then hybridized to variable number of tandem repeat (VNTR) probes to examine the effect of the storage conditions on the membrane-bound DNAs. It was shown that such membranes could be successfully hybridized and rehybridized if they were stored at -20 or 4 degrees C, but storage under ambient conditions reduced or eliminated the likelihood of successful hybridization.

Autoradiography↗
PubMed1991

Tracking the violent criminal offender through DNA typing profiles--a national database system concept.

Implementation of standard methods for the conduct of restriction fragment length polymorphism analysis into the protocols of United States crime laboratories offers an unprecedented opportunity for the establishment of a national computer database system to enable interchange of DNA typing information. The FBI Laboratory, in concert with crime laboratory representatives, has taken the initiative in planning and implementing such a database system. The Combined DNA Index System (CODIS) will be composed of three sub-indices: a statistical database, which will contain frequencies of DNA fragment alleles in various population groups; an investigative database which will enable linkage of violent crimes through a common subject; and a convicted felon database that will serve to maintain DNA typing profiles for comparison to profiles developed from violent crimes where the suspect may be unknown.

Computer Communication Networks↗
PubMed1991

Genetic typing using automated electrophoresis and fluorescence detection.

Multi-color fluorescence detection systems offer unique advantages when compared to single label detection methods for DNA typing, genetic disease testing, population fingerprinting, and DNA mapping. Internal controls are easily used and identified by different color dye labels. Multiple independent samples or multiple analyses of the same sample are run in each lane of a gel. Precision of size assignment and quantification are improved. Here, we will review a variety of methods used to analyze DNA and present the advantages of the multi-color fluorescence dye approach. An automated and quantitative DNA typing assay for human identification is shown. This method is an improvement over previous manual techniques and uses multi-color fluorescence labeling, electrophoresis and real-time detection methodology.

Analog-Digital Conversion↗
PubMed1991

Extraction strategy for obtaining DNA from bloodstains for PCR amplification and typing of the HLA-DQ alpha gene.

A simple, practical approach for the extraction of PCR-amplifiable DNA for the HLA-DQ alpha gene from bloodstains deposited on various substrates is described. DNA from bloodstains is purified using Chelex 100 ion-exchange resin and then amplified. If amplification is not achieved, the extract is washed through a Centricon 100 dialysis/concentration tube. If the second amplification of this extract produces a negative result, the extract is processed with Chelex 100 again. This approach has been found to be reliable, safe, efficient and economical.

Blood Stains↗
PubMed1991

The distribution of the HLA-DQ alpha alleles and genotypes in the Finnish population as determined by the use of DNA amplification and allele specific oligonucleotides.

Allele and genotype frequencies for the HLA-DQ alpha locus were determined for use in forensic analyses and paternity tests in Finland. The polymerase chain reaction (PCR) and the reverse dot blot format were employed to detect 6 different HLA-DQ alpha alleles. All 6 HLA-DQ alpha alleles were detected among the 112 unrelated individuals with allele frequencies ranging from 5.8% to 32.6%. The distribution of the observed genotypes is in Hardy-Weinberg equilibrium. Additionally, this Finnish population sample is statistically similar to 2 other Caucasian sample populations. The power of discrimination of this system in the Finnish population sample is 0.92, suggesting this method may prove suitable for identification purposes.

Alleles↗
PubMed1991

PCR-based typing of DNA extracted from cigarette butts.

Limited genetic marker information can be obtained from saliva by typing by conventional serological means. Thus, the application of PCR-based DNA typing methods was investigated as a potential approach for typing genetic markers in saliva. DNA was isolated from 200 cigarettes smoked by 10 different individuals (20 cigarettes per individual) and from 3 cigarette butts recovered from 2 crime scenes (adjudicated cases) using a Chelex 100 extraction procedure. The amount of recovered human DNA was quantified by slot-blot analysis and ranged from approximately less than 2-160 ng DNA per cigarette butt for the 200 samples, and 8 ng, 50 ng, and 100 ng for the cigarette butts from the adjudicated cases. The DNA was successfully amplified by the polymerase chain reaction (PCR) for the HLA-DQ alpha locus (99 out of 100 samples) as well as for the variable number of tandem repeat (VNTR) locus D1S80 (99 out of 100 samples). Amplification and typing of DNA was successful on all samples recovered from the crime scenes. The results suggest that PCR-based typing of DNA offers a potential method for genetically characterizing traces of saliva on cigarette butts.

DNA↗
PubMed1991

The polymerase chain reaction and post-mortem forensic identity testing: application of amplified D1S80 and HLA-DQ alpha loci to the identification of fire victims.

The application of DNA typing methods after amplification by the polymerase chain reaction (PCR) of DNA derived from body tissues from charred fire victims was investigated. A total of 26 different tissue specimens from ten extensively burned individuals were analyzed. The samples included femoral muscle, psoas muscle, bone marrow and blood. The post-mortem period varied from 38 to 183 h. After amplifying the DNA by PCR from the various tissues, the D1S80 locus was analyzed with a high resolution polyacrylamide gel electrophoresis technique followed by silver staining and the alleles of the HLA-DQ alpha locus were detected by using a reverse dot blot format. All samples could be typed for both loci and the genotypes were consistent in the various tissues from each individual. A parentage test was performed in two cases and Mendelian inheritance of the alleles for both loci was observed.

Alleles↗
PubMed1991

Identification of individuals with DNA testing.

The fast technical development in molecular biology and the increasing knowledge of the human genome has had a major impact on forensic medicine. Genetic characterization of individuals at the DNA level enables identity testing from a minimal amount of biological specimen in cases of sexual assault, homicide, and unknown human remains. Also paternity testing is changing from level of gene products to the genomic level. This article addresses some of the advantages of DNA testing over the conventional forensic serology, and the DNA techniques currently used in forensic science.

ABO Blood-Group System↗
PubMed1991

Analysis of the VNTR locus D1S80 by the PCR followed by high-resolution PAGE.

Allelic data for the D1S80 locus was obtained by using the PCR and subsequent analysis with a high-resolution, horizontal PAGE technique and silver staining. Compared with RFLP analysis of VNTR loci by Southern blotting, the approach described in this paper offers certain advantages: (1) discrete allele resolution, (2) minimal measurement error, (3) correct genotyping of single-band VNTR patterns, (4) a nonisotopic assay, (5) a permanent record of the electrophoretic separation, and (6) reduced assay time. In a sample of 99 unrelated Caucasians, the D1S80 locus demonstrated a heterozygosity of 80.8% with 37 phenotypes and 16 alleles. The distribution of genotypes is in agreement with expected values according to the Hardy-Weinberg equilibrium. Furthermore, the observed number of alleles and the level of heterozygosity, obtained through the protocol described here, were congruent with each other in accordance with the expectation of a mutation-drift equilibrium model for a single, homogeneous, random-mating population. Therefore, the analysis of D1S80 and similar VNTR loci by amplified fragment length polymorphism (AMP-FLP) may prove useful as models for population genetic issues for VNTR loci analyzed by RFLP typing via Southern blotting.

Blotting, Southern↗
PubMed1991

Fixed-bin analysis for statistical evaluation of continuous distributions of allelic data from VNTR loci, for use in forensic comparisons.

The detection of DNA polymorphisms by RFLP analysis is having a major impact on identity testing in forensic science. At present, this approach is the best effort a forensic scientist can make to exclude an individual who has been falsely associated with an evidentiary sample found at a crime scene. When an analysis fails to exclude a suspect as a potential contributor of an evidentiary sample, a means should be provided to assess suitable weight to the putative match. Most important, the statistical analysis should not place undue weight on a genetic profile derived from an unknown sample that is attributed to an accused individual. The method must allow for limitations in conventional agarose-submarine-gel electrophoresis and Southern blotting procedure, limited sample population data, possible subpopulation differences, and potential sampling error. A conservative statistical method was developed based on arbitrarily defined fixed bins. This approach permits classification of continuous allelic data, provides for a simple and portable data-base system, and is unlikely to underestimate the frequency of occurrence of a set of alleles. This will help ensure that undue weight is not placed on a sample attributed to an accused individual.

Alleles↗
PubMed1991

Effects of presumptive test reagents on the ability to obtain restriction fragment length polymorphism (RFLP) patterns from human blood and semen stains.

Some of the commonly used presumptive test reagents for identification of blood and semen could potentially affect the recovery of intact high-molecular-weight deoxyribonucleic acid (DNA) from evidentiary samples. Thus, the capability of performing restriction fragment length polymorphism (RFLP) analysis on evidentiary samples could be compromised. In order to investigate the potential effects of presumptive test reagents on the DNA present in these samples, bloodstains on cotton and glass were exposed directly to luminol, benzidine, phenolphthalein, o-tolidine, and leucomalachite green, while semen stains and vaginal swabs containing semen were exposed directly to bromochloroindolyl phosphate (BCIP) and sodium thymolphthalein monophosphate (STMP) reagents. The yield gels for DNA quality and quantity and RFLP results indicated that bloodstains exposed to luminol, benzidine dissolved in ethanol, and phenolphthalein, as well as semen stains and vaginal swabs exposed to BCIP and STMP yield RFLP patterns consistent with that of the uncontaminated control. Except for the phenolphthalein treatment, the quantity of extractable, high-molecular-weight DNA obtained was comparable with that of untreated stains. Therefore, evidentiary material purposely or inadvertently contaminated with these reagents can be successfully typed. However, stains exposed to benzidine dissolved in glacial acetic acid, leucomalachite green, and o-tolidine failed to yield high-molecular-weight DNA or to produce any RFLP patterns.

Aniline Compounds↗
PubMed1991

Deoxyribonucleic acid (DNA) analysis by restriction fragment length polymorphisms of blood and other body fluid stains subjected to contamination and environmental insults.

Deoxyribonucleic acid (DNA) restriction fragment length polymorphism (RFLP) profile results were obtained from bloodstains and other body fluid stains subjected to mixture with other body fluids, environmental insults (sunlight and temperature), different substrates (cotton, nylon, blue denim, glass, aluminum, and wood), and contaminants (gasoline, bleach, sodium hydroxide, soil, motor oil, detergent, phosphate salt, glacial acetic acid, and microorganisms). Of the samples that produced profile results, all had profiles that were consistent with those of untreated control samples.

Blood Stains↗
PubMed1991

Validation studies on the analysis of the HLA DQ alpha locus using the polymerase chain reaction.

A series of experiments has been performed to evaluate typing of the HLA DQ alpha gene by polymerase chain reaction (PCR) amplification of the gene and subsequent hybridization with sequence-specific oligonucleotide probes. These experiments were designed to evaluate DQ alpha typing for analysis of evidentiary specimens. Bloodstains were exposed to a variety of conditions and environmental insults. These conditions included exposure to many different types of substrates, various microorganisms that could be encountered in evidentiary stains, sunlight, and a variety of chemical contaminants. Varying amounts of genomic deoxyribonucleic acid (DNA) were amplified to test the sensitivity of DQ alpha typing. The sensitivity of the PCR technique raises the concern that DNA from sources other than the evidentiary material could be detected. A series of experiments was done to evaluate the question of DNA contamination. Purified DNA samples with different DQ alpha types were mixed in different ratios to determine the ratio at which it could not be determined whether an allele was from the sample or the contaminant. Samples were exposed to a variety of situations that could lead to contamination, such as extensive handling and exposure to coughing or sweaty clothing, to other wet bloodstains, and to saliva. The DQ alpha types were determined from 469 individuals from three sample populations (Caucasian, black, and Hispanic), and the genotype frequencies were compared with frequencies previously reported by others. DNA samples from old cases [which had previously been analyzed by restriction fragment length polymorphism (RFLP) typing of variable number of tandem repeat sequences] were typed. All samples that were excluded by DQ alpha typing were also excluded by RFLP analysis, and all samples that were included by RFLP analysis were included by DQ alpha typing. Finally, the problem of allele dropout, or the failure to detect particular alleles, was noted and alleviated by performing the typing under appropriate conditions. The results of these validation experiments indicate that typing of the DQ alpha gene by PCR and detection of specific alleles can be accomplished, when the typing is done using proper protocols, without producing false positive or false negative results.

Algorithms↗
PubMed1991

Typing of deoxyribonucleic acid (DNA) extracted from compact bone from human remains.

The application of deoxyribonucleic acid (DNA) typing methods for the potential identification of unknown human remains was investigated. DNA was isolated from compact bone tissue from badly decomposed bodies and from known and unknown human remains, using a decalcification and ion wash procedure. Restriction fragment length polymorphism (RFLP) analysis of variable number of tandem repeats (VNTR) loci yielded results in some cases, but more often the DNA was too degraded to produce RFLP patterns. No RFLP profiles could be obtained from putrefied soft tissues. However, DNA extracted from compact bone tissue of human remains up to eleven years old was successfully amplified using the polymerase chain reaction (PCR) for the VNTR loci D1S80, D17S5, COL2A1, and APO B, as well as the HLA-DQ alpha locus. This is especially significant, since PCR results were obtained from those samples whose DNA had been degraded substantially and had yielded no RFLP patterns. All DNA types determined from the compact bone tissue from decomposed bodies whose identification had been established first by other means (and whose parents or offspring were available for typing) demonstrated mendelian inheritance of the alleles of the loci analyzed. These results suggest that amplification and typing of DNA extracted from compact bone of human remains could be useful in establishing the identity of a person, as well as in excluding possible false identifications.

Bone and Bones↗
PubMed1990

Applying highly polymorphic variable number of tandem repeats loci genetic markers to identity testing.

The detection of alleles of variable number of tandem repeats (VNTR) loci by restriction fragment length polymorphism analysis has become an important aspect of genetic characterization for identity testing. Some VNTR loci are so polymorphic that the analysis of three to five genetic markers could potentially provide unique identity. However, the more informative a genetic marker is (i.e., high degree of polymorphisms), the better it is as an exculpatory tool. This approach currently provides the best avenue for excluding a falsely associated individual with a particular sample. When an analysis fails to exclude an individual as the source of the questioned material, a value (frequency of occurrence) should be placed on the VNTR profiles to assess weight to the inclusion in identity testing. Arbitrarily defined fixed bins were designed to accommodate quasi-continuous data and to provide a result that would not place an underestimation of the frequency of occurrence of a set of alleles attributed to an individual.

Alleles↗