King Tut’s Family Secrets Kuei-Chiu Chen, Premedical Program, Weill Cornell Medical College in Qatar Their bodies have lain here in the Valley of the Kings near Luxor, Egypt, for more than 3,000 years. The flesh on many of them is still present as a result of embalming. The walls of their burial chambers are covered with ornate paintings of gods that were said to greet them in the other world, and the lavishly decorated objects of gold and precious stones buried with them were intended for their use in the afterlife. These are the mummies of the royal families of ancient Egypt. One of the members, the “Boy King” – King Tutankhamun – became pharaoh at the age of nine or ten and died when he was still a teenager. Other tombs in the Valley of the Kings contain other royal mummies. Is “King Tut” related to any of these mummies? 2 Discovery of Satellite DNA • Genomic DNA is fragmented and centrifuged. • When reaching equilibrium, DNA bands settle based on density. Uniform Gradient DNA fragments Centrifugation Satellite bands of DNA Main band of DNA Cell debris 3 DNA from the satellite bands was named satellite DNA. Satellite DNA consists of highly repetitive sequences found mostly in centromeres and telomeres. 4 • The length of repeat unit varies in satellite DNA. • DNA with repeat unit from 2 to 6 bases long is called microsatellite DNA because the repeat sequence is shorter. • The term microsatellite DNA is based on the historical term of satellite DNA. The location of microsatellite is mostly NOT found on centromeres or telomeres of the chromosomes. 5 Terms in genetics: example in human chromosomes Homologous chromosomes (one from father and one from mother) Locus is the specific position on the chromosome. Locus (heterozygous: having two different alleles) Allele is alternative form of a gene at a locus. Homozygous: having the same allele at a locus. Heterozygous: having different alleles at a locus. 6 Types of Microsatellites Those with two-base repeat unit CGACTAGCCACGTGTGTGTGTGTGTGTGTGTGTACAGGACTTAGC 11 repeats (allele 11) Those with three-base repeat unit TTCTAGCCGCTTGTTGTTGTTGTTGTTGTTGTTGCCAGTACTCAG 8 repeats (allele 8) Those with four-base repeat unit GCGAAGTTCCGAATGAATGAATGAATGAATGAATGAATGCCGCATT 7 repeats (allele 7) Most microsatellite DNA loci used in human identification have 4-base pair repeats. Microsatellites are also called Short Tandem Repeats (STRs). 7 CQ#1: A person has the following microsatellite sequence on one chromosome: Repeat region GCGAAGTTCCGGATGGATGGATGGATGGATGGATGCCGCATT What is the sequence of the repeat unit? A. B. C. D. E. ATG GATG ATGGAT GGATGG None of the above 8 The genotype of a person for each locus is shown as the number of repeat units he/she carries. Since a person is diploid and has a pair of homologous chromosomes, the genotype is shown as two numbers. - Genotype 6, 8: For a person heterozygous at a locus where there are 6 repeats on one chromosome and 8 repeats on the other chromosome within the homologous pair. - Genotype 7, 7: For a person homozygous at a locus where there are 7 repeats on both of his/her homologous chromosomes. 9 Repeat sequences Person A Genotype 7, 7 (7 repeats, 7 repeats) Person B Genotype 6, 8 (6 repeats, 8 repeats) 10 CQ#2: If this person’s homologous chromosomes have the following sequences: Repeat region GCGAAGTTCCGGATGGATGGATGGATGGATGCCGCATT CGCTTCAAGGCCTACCTACCTACCTACCTACGGCGTAA GCGAAGTTCCGGATGGATGGATGGATGGATGGATGGATGCCGCATT CGCTTCAAGGCCTACCTACCTACCTACCTACCTACCTACGGCGTAA What is this person’s genotype for this locus? A. 5, 7 B. C. D. E. 5, 5 7, 7 GATG, GATG CTAC, CTAC 11 Slippage during DNA replication creates variation in number of repeat units Normal replication A Slippage in new strand New strand GAC GAC GAC GAC GAC GAC CTG CTG CTG CTG CTG CTG Template strand Next replication C G GAC GAC GAC GAC GAC GAC CTG CTG CTG CTG CTG CTG Insertion mutation (n+1) GAC GAC GAC GAC GAC GAC GAC CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG GAC GAC GAC GAC GAC GAC Normal length Next replication Slippage in template GAC GAC GAC GAC GAC CTG CTG CTG CTG CTG C G T Deletion mutation (n-1) CTG CTG CTG CTG CTG GAC GAC GAC GAC GAC CTG CTG CTG CTG CTG CTG GAC GAC GAC GAC GAC GAC Normal length 12 Microsatellite DNA is highly variable between individuals. Variation forms the basis for individual identification. Alleles (number of repeats) Locus Name TPOX D3S1358 FGA CSF1PO 7 14 18 8 8 15 19 9 9 16 20 10 10 17 21 11 11 18 22 12 23 13 24 14 25 15 12 26 27 28 13 Polymerase Chain Reaction (PCR) An in vitro reaction (cell-free) Required materials: - template: the DNA sequence to be copied - dNTPs (dATP, dGTP, dCTP, and dTTP) as building blocks - primers: short DNA sequences (19-33 bases in STRs) complementary to the template to start the reaction - DNA polymerase: enzyme to catalyze the reaction Forward primer DNA Reverse primer 14 Extraction of DNA from Ancient Mummies Challenges: 1. DNA degradation: by physical, chemical, and biological causes. 2. Contamination: cells from other persons who contacted the mummies from ancient to modern time. Solutions? 1. Use deep tissues that were less degraded and less likely to be contaminated, such as bone. 2. All researchers who handled the mummies should have their DNA profile analyzed for use as reference samples. 3. Have multiple labs conduct the same PCR and compare results. 15 Temperature Profile for PCR 94C 55C 72C 16 The number of PCR product increases exponentially following the number of thermal cycles. 0 cycle 1 molecule 1 cycle 2 molecules (21) 2 cycles 3 cycles 4 molecules (22) 8 molecules (23) If starting with one molecule, the final number of double stranded molecule is 2n. 17 Polymerase Chain Reaction Animation http://www.sumanasinc.com/webcontent/animations/content/pcr.html 18 CQ#3: If you start with 1 double-stranded DNA molecule as a template and conduct a PCR for 4 thermal cycles, how many DNA molecules of the PCR product will be there at the end of the reaction? A. B. C. D. E. 12 16 24 48 96 19 CQ#4: If you start with 3 double-stranded DNA molecules as a template and conduct a PCR for 4 thermal cycles, how many DNA molecules of the PCR product will be there at the end of the reaction? A. B. C. D. E. 12 16 24 48 96 20 Composition of a PCR product from a locus The length of a PCR product consists of the forward primer, reverse primer, repeat sequences and flanking sequences. Forward primer binding site Reverse primer binding site Repeat sequences 3’ 5’ Flanking sequence Flanking sequence 5’ 3’ Length of PCR products 21 Sample from a person homozygous at the locus will produce PCR fragments of one length Person A Genotype 7, 7 Length of PCR products 22 Sample from a person who is heterozygous at a locus will produce PCR fragments of two different lengths Length of PCR products Person B Genotype 6, 8 Length of PCR products Allele 6 fragments Allele 8 fragments 23 CQ#5: In the picture below, if each of the repeat sequences is 4 base-pair long, what is the total length of the PCR product? bp = base pairs 5 repeat sequences 3’ 5’ 20 bp 5’ 25 bp 35 bp A. B. C. D. E. 60 bp 3’ 100 115 135 145 160 24 DNA Structure Phosphate groups give DNA its negative charge 25 Gel Electrophoresis - Gel made of agarose forms a matrix. - DNA sample is loading into a well on the gel as shown in A. - Phosphate groups on DNA carry negative charges. - After applying power, DNA fragments migrate to the positive electrode, shown in B. - Fragments are separated based on their sizes, smaller fragments moving faster while larger fragments moving more slowly. - Fragments of the same size will settle at the same location on the gel. 26 • DNA bands do not have colors. • Ethidium bromide (a chemical) inserts itself between DNA bases. • When a gel stained with ethidium bromide is put on a UV table, DNA bands glow orange light. • Photography of the gel produces pictures in which DNA bands are white on a dark background. • The brighter the DNA bands, the more molecules there are in the bands. Sizing ladders (standard) 27 Ethidium Bromide A very planar molecule that can insert itself between DNA bases. 28 CQ6. A person has the genotype of 9, 9 on one of his microsatellite loci. An electrophoresis was conducted on the PCR products of this locus. Which lane on the gel below is most likely the result of the PCR fragments? (L: size ladder) L A B C D 29 Analysis of one locus is often insufficient to definitively identify a person, so multiple loci are required. Eight loci were amplified in the seven Egyptian mummies, each locus requiring one specific pair (two unique sequences) of primers. D2S1338 FGA CSF1PO D7S820 D13S317 D16S539 D18S51 D21S11 30 Conventional agarose gels have difficulty detecting small differences in fragment size. Example: Genotype 7, 8 Using other gel medium in conjunction with automated PCR, the person’s genotype may be analyzed accurately and quickly. 31 Capillary tube (-) Larger fragment DNA Analyzers Detector Laser Smaller fragment (+) 32 Results from DNA Analyzer If rotate counterclockwise… Smaller fragments Locus 1 181 193 90° Larger fragment Locus 2 225 Locus 3 278 286 Heterozygous (two peaks) Homozygous (one peak) Heterozygous (two peaks) 33 286 Locus 3 278 225 193 Height of the peak is equivalent to the intensity of the DNA band and the quantity of DNA molecules on a gel. 181 Smaller fragments Locus 1 Locus 2 Larger fragment Location of hypothetical well in a gel 34 The Mystery of Tutankhamun’s Family Tree 35 The Seven Mummies Amenhotep III KV35YL Tiye Thuya Akhenaten Tutankhamun Yuya 36 In a known parentage relationship, you can trace which allele is passed down from each of the parents to the child. 13, 15 14, 17 13, 17 37 CQ7. The following are the results of an analysis on two microsatellite loci from a mother, a father and their child. Which one is the child of the other two? (Number below each peak is the size of that fragment in base pair.) Locus 1 Locus 2 A 190 194 282 286 B 290 190 198 C 194 198 286 290 38 Seven strips of paper showing genotypic profiles similar to the following will be distributed to each group. Locus Female D13S317 Tiye 11 Name 12 D7S820 10 15 D2S1338 22 26 D21S11 26 29 D16S539 6 11 D18S51 19 22 CSF1PO 9 12 FGA 20 26 Allele 39 D13S317 Tutankhamun Yuya 10 12 Amenhotep III KV35YL 16 26 D2S1338 11 6 22 13 9 12 11 12 15 D7S820 10 13 D7S820 10 15 27 D2S1338 19 26 D2S1338 22 26 D13S317 D7S820 D2S1338 10 6 16 16 D13S317 Akhenaten 15 D7S820 D13S317 Tiye 10 D2S1338 D13S317 D13S317 Thuya D7S820 10 12 15 D7S820 15 15 27 D2S1338 16 26 D13S317 D7S820 D2S1338 10 6 16 12 10 26 D21S11 29 34 D21S11 29 34 D21S11 26 35 D21S11 26 29 D21S11 25 34 D21S11 29 34 D21S11 25 29 D16S539 8 13 D16S539 6 10 D18S51 19 19 D18S51 12 22 CSF1PO 6 12 CSF1PO 9 12 D16S539 D18S51 CSF1PO 11 8 7 13 D16S539 6 11 D16S539 8 13 D16S539 11 13 D16S539 8 11 19 D18S51 19 22 D18S51 16 22 D18S51 16 19 D18S51 16 19 12 CSF1PO 9 12 CSF1PO 6 9 CSF1PO 9 12 CSF1PO 6 12 FGA 23 23 FGA 20 Genotypic profiles of King Tut and six family members. 25 FGA 24 26 FGA 20 26 FGA 23 31 FGA 20 23 FGA 20 23 40 Exercise 1: Determine the members in King Tut’s family tree Male Female Marriage Giving rise to descendant Giving rise to two descendants Sibling marriage 41 The family tree has been determined But how confident are you in this family tree? Paternity index (or maternity index if the paternity is certain) 42 If only one of the parents is known, the allele in the child not found in one of the parents must have come from the other parent. This allele is called the obligate allele. 14, 17 13, 17 43 SAQ 1. Determine the obligate allele of each of the loci. Determine the partial genotype of the father. sample locus Mother Child CSF1PO 10, 11 10, 13 TPOX 5, 5 5, 11 D7S820 12, 15 12, 12 D13S317 8, 10 10, 11 44 CQ8. Which of the accused men is more likely to be the father of the child? A or B? sample locus CSF1PO Mother Accused Accused Child Man A Man B 10, 11 10, 13 10, 17 13, 21 5, 5 5, 11 6, 7 6, 11 D7S820 12, 15 12, 12 7, 15 8, 12 D13S317 8, 10 10, 11 9, 15 11, 11 TPOX 45 You have determined that one of the men in the previous slide is a possible father to the child. But how certain are you? In legal situations, Paternity Index (or Parentage Index, PI) is often used to provide mathematical certainty to parentage. PI is applied only when an accused man is a match by having the set of obligate alleles. 46 Alleged father Mother AB CD BC Child Paternity Index (PI) = Probability of passing the obligate allele given the alleged man is the father (X) Probability of a random man in the population passing the obligate allele to 47 the child (Y) PI = X Y X = 0.5 if the alleged father is heterozygous for the obligate allele; 1.0 if the alleged father is homozygous for the obligate allele Y = the frequency of the obligate allele found in the population X and Y are two competing hypotheses; the higher the X is and the lower the Y is, the greater the PI will be, and stronger the implication that the alleged man is the father of the child. 48 If the alleged father is heterozygous for the obligate allele….. Alleged father Mother AB CD 0.5 BC Child 0.5 Paternity Index = pC pC – probability of allele C, which is the frequency of allele C in the population 49 If the alleged father is homozygous for the obligate allele….. Alleged father Mother AB CC 1.0 BC Child 1.0 Paternity Index = pC 50 SAQ2. The tables below list the genotype of a locus from three people involved in a paternity case and the frequency of each of the alleles of this locus in the entire population. (Frequency here is a number ranging from 0 to 1.) What is the paternity index? Allele Frequency 6 0.10 Individual Genotype 7 0.01 Mother 8, 9 8 0.37 Child 8, 11 9 0.18 Accused man 6, 11 10 0.09 11 0.21 12 0.02 Total 1.00 51 If the mother and the child are heterozygous and share both alleles, we don’t know which of the two alleles is actually the allele that has been passed on by the mother. Because of this uncertainty, either of the alleles could be from the mother, and the other allele would be from the father. In probability, if either of the two events could be true, the probability for either of the events to take place is the sum of the individual probability of the event. 52 If the mother and the child share both heterozygous alleles…. Mother AB AB Child If the mother passed allele A to the child, then the probability of a random man passing allele B to the child is the frequency of allele B in the population, or pB. If the mother passed allele B to the child, then the probability of a random man passing allele A to the child is the frequency of allele B in the population, or pA. 53 If the mother and the child share both heterozygous alleles…. Alleged father Mother AB BC 0.5 AB Child 0.5 Paternity Index = Probability of a random man passing allele A pA + pB or Probability of a random man passed allele B 54 • Multiple markers are often used simultaneously to increase the certainty of parentage. • If these markers are not linked genetically, multiplication rule may be applied to all the paternity indices. • The mathematical product of paternity indices is called combined paternity index. D2S1338 FGA CSF1PO D7S820 D13S317 D16S539 D18S51 D21S11 55 CQ9. If you want to use PCR technique to amplify markers located on six unlinked locations on the chromosomes, how many total unique primer sequences do you need? A. 1 B. 3 C. 6 D. 8 E. 12 56 Combined Paternity Index = PI1 x PI2 x …x PIn Combined paternity index in theory can reach infinity if number of loci used in the analysis is large. In forensic community, paternity is accepted if CPI > 100 It essentially means that the alleged man is100 times or more likely than a randomly selected man to be the father of the child. 57 SAQ3. If the three people involved in a paternity dispute have the genotypic profiles shown in the following table, determine the formula for the combined paternity index (CPI). Note, use the appropriate symbols, e.g., P8 to indicate the frequency of allele 8.) TPOX D3S1358 CSF1PO Mother 8, 9 16, 17 10, 12 Child 9, 10 16, 16 10, 11 Accused man 10, 10 15, 16 11, 11 58 SAQ4. If the CPI formula is the one listed below, what is the CPI value based on the frequency of each allele in the table? Locus and frequency of each allele 1.0 0.5 1.0 CPI = ´ ´ P10 P16 P11 Allele TPOX D3S1358 CSF1PO 6 0.10 - - 7 0.01 - - 8 0.37 - 0.01 9 0.18 - 0.01 10 0.09 - 0.21 11 0.21 - 0.30 12 0.02 - 0.36 13 - - 0.10 14 - 0.04 0.01 15 - 0.37 - 16 - 0.37 - 17 - 0.16 - 18 - 0.06 - Total 1.00 1.00 1.00 59 SAQ5. Again, based on the same CPI formula below, which of the three loci produces the highest PI value so that it makes the greatest impact on the CPI value? Why? Locus and frequency of each allele 1.0 0.5 1.0 CPI = ´ ´ P10 P16 P11 Allele TPOX D3S1358 CSF1PO 6 0.10 - - 7 0.01 - - 8 0.37 - 0.01 9 0.18 - 0.01 10 0.09 - 0.21 11 0.21 - 0.30 12 0.02 - 0.36 13 - - 0.10 14 - 0.04 0.01 15 - 0.37 - 16 - 0.37 - 17 - 0.16 - 18 - 0.06 - Total 1.00 1.00 1.00 60 SAQ6. If the CPI is < 100 from the analysis of three loci, what is the best course of action or conclusion? 61 SAQ7. Now calculate the combined paternity index on the first three members in the family tree using the provided Egyptian allele frequency handout. You may choose either one of the parents as the unknown. If the obligate allele is not found in the table, skip that locus. We will discuss this later. 62 DISCUSSION: What are the possible reasons that some alleles in the members are not found in the Egyptian allele frequency table provided? 63 Image Credits Unless specified differently below, images were created by the case author. Slide 1 Description: King Tut Ankh Amun Golden Mask. Source: Steve Evans, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:King_Tut_Ankh_Amun_Golden_Mask.jpg Clearance: Used in accordance with the Creative Commons Attribution 2.0 Generic license. Slide 2 Description: Mural from KV62 in Valley of the Kings. Source: Kenneth Atherton and family, http://www.theathertons.info/2010/06/the-valley-of-the-kings/ Clearance: Used in accordance with the Creative Commons Attribution-Noncommercial-Share Alike 3.0 United States License. Slides 4, 6, 30 Description: Normal male human karyotype. Source: National Cancer Institute, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Karyotype_%28normal%29.jpg Clearance: This image is a work of the National Institutes of Health, part of the United States Department of Health and Human Services. As a work of the U.S. federal government, the image is in the public domain. Slide 15 Description: Mummy on display at the Philadelphia Academy of Natural Sciences. Source: By “Smallbones,” accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Mummy_PANS.JPG Clearance: Released into public domain by the photographer. Slide 25 Description: DNA strand showing Chemical structure of nucleic Acid Bases. Source: By “Boumphreyfr,” accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Dna_strand3.png Clearance: Used in accordance with the Creative Commons Attribution-Share Alike 3.0 Unported license. Slide 26 Description: Diagram illustrating gel electrophoresis procedure. Source: By “Jjw,” accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Gel_electrophoresis_procedure.png Clearance: Used in accordance with the Creative Commons Attribution-Share Alike 3.0 Unported license. Slide 27 Description: Gel electrophoresis image. Source: By Kuei-Chiu Chen, case author. Clearance: Used with permission. 64 Slide 28 Description: Chemical structure of ethidium bromide. Source: By “Calvero,” accessed on Wikimedia Commons at http://en.wikipedia.org/wiki/File:Ethidium_bromide.svg Clearance: Released into the public domain by the image creator. Slide 32 Description: A row of DNA sequencing machines (3730xl DNA Analyzer machines from Applied Biosystems). Source: This image was originally posted to Flickr by jurvetson at http://www.flickr.com/photos/jurvetson/57080968/, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:DNA-Sequencers_from_Flickr_57080968.jpg. Clearance: Used in accordance with the Creative Commons Attribution 2.0 Generic license. Slides 35 Description: Tutankhamun. Source: Jerzy Strzelecki, http://commons.wikimedia.org/wiki/File:Tutanchamon_(js)_1.jpg Clearance: Used in accordance with the Creative Commons Attribution-Share Alike 3.0 Unported license. Slide 36 Description: Colossal statue of Amenhotep III in the British Museum. Source: Photograph by A. Parrot, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Colossal_Amenhotep_III_British_Museum.jpg Clearance: Released into public domain by photographer. Slide 36 Description: Tiye, Ägyptisches Museum (Egyptian Museum), Berlin. Source: Einsamer Schütze, accessed on Wikimedia Commons at http://en.wikipedia.org/wiki/File:%C3%84gyptisches_Museum_Berlin_027.jpg Clearance: Used in accordance with the Creative Commons Attribution-Share Alike 3.0 Unported license. Slide 36 Description: Akhenaten, Pharaoh of Egypt. Egyptian Museum, Cairo. Source: User:Hajor, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Pharaoh_Akhenaten.jpg Clearance: Used in accordance with the Creative Commons Attribution-Share Alike 1.0 Generic license. Slide 36 Description: Gilded cartonnage mummy mask of Thuya, wife of Yuya and mother of Queen Tiye Source: Jon Bodsworth, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Mummy_mask_of_Thuya.jpg Clearance: Copyright free. 65 Slide 36 Description: KV35YL--Front view of the "Younger Lady Mummy" found in tomb KV35. Source: Image derived from Grafton Elliot Smith’s The Royal Mummies, Plate XCIX, first published in 1912, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:TheYoungerLady-61072-FrontView-PlateXCIX-TheRoyalMummies-1912.gif Clearance: Public domain due to expired copyright. Slides 36 Description: Tutankhamun. Source: Jerzy Strzelecki, http://commons.wikimedia.org/wiki/File:Tutanchamon_(js)_1.jpg Clearance: Used in accordance with the Creative Commons Attribution-Share Alike 3.0 Unported license. Slide 36 Description: The gilded cartonnage mummy mask of Yuya, the father of Queen Tiye. Yuya was the father-in-law of pharaoh Amenhotep III, one of the most powerful kings of Egypt’s 18th dynasty. Source: Jon Bodsworth, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Mummy_mask_of_Yuya.jpg Clearance: Copyright free. Slides 37 and 43 Description: Cropped screenshot of Richard Burton and Elizabeth Taylor from the trailer for the film Cleopatra. Source: Jon Bodsworth, accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:1963_Cleopatra_trailer_screenshot_%2823%29.jpg Clearance: This work is in the public domain because it was published in the United States between 1923 and 1963 and although there may or may not have been a copyright notice, the copyright was not renewed. Unless its author has been dead for the required period, it is copyrighted in the countries or areas that do not apply the rule of the shorter term for US works, such as Canada (50 pma), Mainland China (50 pma, not Hong Kong or Macao), Germany (70 pma), Mexico (100 pma), Switzerland (70 pma), and other countries with individual treaties. Slides 37 and 43 Description: Sleeping infant. Source: Andrés Nieto Porras from Palma de Mallorca, España, (cropped and tinted), accessed on Wikimedia Commons at http://commons.wikimedia.org/wiki/File:Sleeping_newborn_infant.jpg Clearance: Used in accordance with the Creative Commons Attribution-Share Alike 2.0 Generic license. 66