Estimating minimum allele frequencies for DNA profile frequency estimates for PCR-based loci

In order that there can be confidence that DNA profile frequency estimates will not place undue bias against a defendant, 2 methods are described for estimating minimum allele frequency bounds for PCR-based loci. One approach estimates minimum allele frequencies for VNTR and STR loci using sample size and the observed heterozygosity at a locus, while the second approach, appropriate for loci typed with allele-specific oligonucleotide probes, is based only on sample size. The use of a minimum allele frequency enables compensation for sparse sampling of infrequent alleles in population databases.

[1]  R. Chakraborty,et al.  D1S80 population data in African Americans, Caucasians, southeastern Hispanics, southwestern Hispanics, and Orientals. , 1995, Journal of forensic sciences.

[2]  B S Weir Independence of VNTR alleles defined as floating bins. , 1992, American journal of human genetics.

[3]  B S Weir,et al.  Independence of VNTR alleles defined as fixed bins. , 1992, Genetics.

[4]  K. Klinger,et al.  Characterization and rapid diagnostic analysis of DNA polymorphisms closely linked to the cystic fibrosis locus. , 1990, Clinical chemistry.

[5]  J. A. Lindsey,et al.  Validation and population studies of the loci LDLR, GYPA, HBGG, D7S8, and Gc (PM loci), and HLA-DQ alpha using a multiplex amplification and typing procedure. , 1995, Journal of forensic sciences.

[6]  Ann E. Blechl,et al.  Human fetal g γ- and A γ-globin genes: Complete nucleotide sequences suggest that DNA can be exchanged between these duplicated genes , 1980, Cell.

[7]  B Budowle,et al.  Analysis of the VNTR locus D1S80 by the PCR followed by high-resolution PAGE. , 1991, American journal of human genetics.

[8]  K. Mullis,et al.  Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. , 1985, Science.

[9]  M. Nei,et al.  MOLECULAR POPULATION GENETICS AND EVOLUTION , 1976 .

[10]  E. Boerwinkle,et al.  VNTR allele frequency distributions under the stepwise mutation model: a computer simulation approach. , 1993, Genetics.

[11]  L. Jin,et al.  Genetic variation at five trimeric and tetrameric tandem repeat loci in four human population groups. , 1992, Genomics.

[12]  R. Chakraborty,et al.  Sample size requirements for addressing the population genetic issues of forensic use of DNA typing. , 1992, Human biology.

[13]  A. Kloosterman,et al.  PCR-amplification and detection of the human D1S80 VNTR locus Amplification conditions, population genetics and application in forensic analysis , 2022 .

[14]  H A Erlich,et al.  Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Motoo Kimura,et al.  A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population*. , 1973, Genetical research.

[16]  N. Huang,et al.  Chinese population data on three tetrameric short tandem repeat loci--HUMTHO1, TPOX, and CSF1PO--derived using multiplex PCR and manual typing. , 1995, Forensic science international.

[17]  Y. Nakamura,et al.  Amplification of a variable number of tandem repeats (VNTR) locus (pMCT118) by the polymerase chain reaction (PCR) and its application to forensic science. , 1990, Journal of forensic sciences.

[18]  D. Russell,et al.  The human LDL receptor: A cysteine-rich protein with multiple Alu sequences in its mRNA , 1984, Cell.

[19]  R. Chakraborty Expected number of rare alleles per locus in a sample and estimation of mutation rates. , 1981, American journal of human genetics.

[20]  K. Mullis,et al.  Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. 1985. , 1992, Biotechnology.

[21]  J. Neel "Private" genetic variants and the frequency of mutation among South American Indians. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[22]  M. Fukuda,et al.  Molecular cloning of a human glycophorin B cDNA: nucleotide sequence and genomic relationship to glycophorin A. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Crow,et al.  THE NUMBER OF ALLELES THAT CAN BE MAINTAINED IN A FINITE POPULATION. , 1964, Genetics.

[24]  R. Chakraborty,et al.  D1S80 allele frequencies in a Chinese population , 1994, International Journal of Legal Medicine.

[25]  W. Ewens The sampling theory of selectively neutral alleles. , 1972, Theoretical population biology.

[26]  N. Freimer,et al.  Allele frequencies at microsatellite loci: the stepwise mutation model revisited. , 1993, Genetics.

[27]  R. Dirnhofer,et al.  Swiss population data on three tetrameric short tandem repeat loci — VWA, HUMTH01, and F13A1 —derived using multiplex PCR and laser fluorescence detection , 2005, International Journal of Legal Medicine.

[28]  R. Reynolds,et al.  Evaluation of the AmpliType® PM DNA Test System on Forensic Case Samples , 1994 .

[29]  H A Erlich,et al.  Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[30]  C. Caskey,et al.  DNA typing and genetic mapping with trimeric and tetrameric tandem repeats. , 1991, American journal of human genetics.

[31]  E. Boerwinkle,et al.  Rapid typing of tandemly repeated hypervariable loci by the polymerase chain reaction: application to the apolipoprotein B 3' hypervariable region. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Lloyd S. Nelson,et al.  Nomograph for Samples Having Zero Defectives , 1978 .

[33]  B. Mccarthy,et al.  High-resolution analysis of a hypervariable region in the human apolipoprotein B gene. , 1989, American journal of human genetics.

[34]  S. Naylor,et al.  Human group-specific component (Gc) is a member of the albumin family. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[35]  B Budowle,et al.  Fixed-bin analysis for statistical evaluation of continuous distributions of allelic data from VNTR loci, for use in forensic comparisons. , 1991, American journal of human genetics.