Eye on DNA — How will it change your life?

Twin DNA Foil Investigators Again

by Dr. Hsien-Hsien Lei
Posted March 21, 2009 in DNA and the Law

Two years ago, identical twin brothers Raymon and Richard Miller both had sex with the same woman who became pregnant. The court decided Raymon was the legal father although the DNA paternity test couldn’t provide definitive proof.

thieves In February, millions of dollars worth of jewelry was stolen in Berlin. Two of the suspects are identical (monozygotic) twins, Hassan and Abbas O. DNA analysis showed that one or both of them were probably at the scene of the crime but it’s impossible to tell. If only one of the brothers is guilty, investigators can’t tell for sure which one it is.

In reality, identical twins do not have perfectly identical DNA due to epigenomic chemical modifications and DNA copy number variations. But until more sophisticated DNA analyses become more widely available or other evidence comes to light, Hassan and Abbas are free and have not been charged. (Spiegel Online via Boing Boing)

Identical twins be forewarned. You may be able to get away with it now, but your time is coming.

NB: In Malaysia, investigators were unable to figure out which one of a pair of identical twins trafficked 166 kilograms of cannabis and 1.7 kilograms of opium. A judge dismissed the case and both twins were set free. (Telegraph)

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DNA Video: Twin DNA Differences

by Dr. Hsien-Hsien Lei
Posted May 17, 2008 in DNA Podcasts and Videos

For more, see my previous post – Genetic Differences Between Identical Twins.

(1 comment)


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Eye on DNA Headlines for 11 April 2008

by Dr. Hsien-Hsien Lei
Posted April 11, 2008 in Eye on DNA Headlines

  • The MIT/Stanford Venture Lab (VLAB) will be hosting DNA for Dollars: Featuring 23andMe, Kleiner Perkins, MDV, and more at Stanford Business School on Tuesday, April 15, 2008 at 6:00 pm.
  • The DNA Network Custom Search Engine has been updated and now includes all 50 member sites.
  • pulitzerCongratulations to New York Times reporter Amy Harmon on her Pulitzer Prize for The DNA Age series of articles on “the impact of genetic technology on American life.”
  • Congratulations also to TR Gregory at Genomicron on his one-year blogging anniversary!
  • Lee Lofland, author of Police Procedure and Investigation, A Guide for Writers shares Things Writers Should Know about DNA. I just have on nitpicky point about the DNA fact that “identical twins have identical DNA”…erm, not quite .
  • Health Content Advisors discusses the role of genetic counselors as healthcare intermediaries.

(>> Start a discussion!)


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Genetic Differences Between Identical Twins

by Dr. Hsien-Hsien Lei
Posted February 20, 2008 in DNA in General

designer babiesIdentical (monozygotic) twins Raymon and Richard Miller had better watch out. The two were embroiled in a paternity suit that alleged both had slept with the same woman on the same day and nobody knew which brother had impregnated her. In May 2007, the judge decided that Raymon is the legal father of the child who was subsequently born although child support was split between the two brothers.

Standard paternity testing examines 16 DNA markers which is enough to make them over 99.99% accurate. In the case of the State of Missouri and Holly Marie Adams vs. Raymon and Richard Miller, the paternity test showed that the two brothers both had a 99.999% probability of being the father. There is currently no commercially available test that can determine which of the twin brothers passed his DNA to the child even though there are ways in which the genomes of identical twins differ.

Epigenomic chemical modifications. Researchers at Ohio State University found epigenetic changes in twins’ genomes that increased as pairs of twins aged. One of the main epigenetic processes that occurs to our DNA is methylation which can be caused by environmental exposures, such as diet and physical activity. Methylation can lead to differences in gene expression and as we age, the amount of DNA methylation increases. So, it’s expected that identical twins will grow less and less similar in their patterns of DNA methylation and gene expression as their lives progress especially if their lifestyle habits and surroundings differ greatly.

DNA copy-number-variation profiles. Another way in which the genomes of identical twins may differ is in copy number variation (CNV) that appears as segments of DNA that are missing, occur in multiple copies, or have flipped orientation in the genome. Identical (monozygotic) twins have been found to have different CNVs which could explain why even identical twins are not truly identical in appearance or other physical characteristics despite similar environmental exposures. For example, one twin sometimes develops a disease while the other does not. (HT: DNA Direct Talk)

What does this mean for Raymon and Richard Miller? DNA methylation patterns and copy number variations can be definitive in a paternity case if differences between the brothers are identified. Then, by comparing the same genomic regions in the child, it may be possible to see who the s/he more closely resembles genetically keeping in mind that the child is also accumulating his/her own DNA methylation and CNVs. While this type of genetic analysis isn’t currently available, it will most likely be available in the child’s lifetime. I would suggest that the Millers’ love child or his/her guardian store DNA from Raymon and Richard Miller for future analysis.

Update:: John Hawks has more.

Photo credit: Wellcome Images under Creative Commons.

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5 Facts (and Caveats) About DNA Profiling

by Dr. Hsien-Hsien Lei
Posted October 24, 2007 in DNA and the Law, DNA in General

Reuters took the trouble to summarize five main facts about DNA profiling and I thought I’d comment on them.

dnaDNA profiling was discovered in 1984 by geneticist Alec Jeffreys of Britain’s Leicester University, who first used it three years later to help solve the murders of Leicestershire schoolgirls Dawn Ashworth and Lynda Mann.

Sir Alec, a 2006 Great Briton, is actually credited with developing DNA fingerprinting specifically.

Here’s a very basic description of how DNA fingerprints were first created using restriction fragment length polymorphisms (RFLP):

1. Extract a sample of DNA from blood, hair, skin, cheek cells, etc.
2. Use polymerase chain reaction (PCR) to create more copies of the DNA to analyze.
3. Use restriction enzymes to cut the DNA strand at specific sequences, which will result in pieces of DNA of varying sizes. Since each person’s DNA unique, the enzymes will cut the DNA in different places and varying sizes of DNA pieces will result.
4. The small pieces of DNA will be passed through an agarose gel which separates them according to size.
5. Compare the DNA patterns created.

dnaThe technology makes use of the fact that small sections of DNA repeat themselves over and over in a way that is unique to each individual. The length of repeats can be measured at different locations to build up an individual’s profile.

There are actually different ways to create a DNA profile. The type of marker mentioned here is the short tandem repeat (STR). Another type of marker that can be used to create a genetic profile is the single nucleotide polymorphism(SNP).

dnaModern genetic tests typically look at 20 “marker” sections of DNA — 10 from the maternal and 10 from the paternal line. The chance of two strangers matching on all 20 is less than one in 1 billion. The chance of a match with a relative, though, is much higher and identical twins have identical profiles.

I’m not really sure what 20 markers this fact is referring to. Law enforcement relies on the Combined DNA Index System (CODIS) that creates DNA profiles from 13 core STR markers. Paternity tests examine as little as three markers to as many as 16. The genotypes at each of the markers would consist of data on two alleles – one from the mother and one from the father.

dnaScientists collect DNA direct from suspects, using a mouth swab, or from the scene of a crime, by gathering traces of blood, semen, hair or saliva. Crime scene samples are more difficult to analyze, since they may be very small and can contain the DNA of several people.

I don’t have much to say about this except that sometimes samples are just plain difficult to analyze whether or not it’s from a crime scene. It all depends on the sample from which the DNA is extracted and the informativeness of the markers being analyzed.

dnaGovernments around the world are building up DNA databases to match suspects with evidence. The United States has the largest database, with over 5 million profiles. But Britain has the highest proportion of people catalogued, with its 4 million records equal to more than 6 percent of the population.

As points of reference, Australia’s national DNA database has over 350,000 DNA samples while New York State has almost 250,000. You may also be interested in these previous posts about the UK national database:

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Genetics of Bipolar Disorder and Hypomania

by Dr. Hsien-Hsien Lei
Posted October 11, 2007 in DNA and Disease

alicia sparksMental Health Notes writer Alicia Sparks, who also has bipolar disorder, celebrated her 26th birthday this week and received this card from her sister:

(COVER)

Sis,
insanity is hereditary.

(Inside)

We are so screwed.

Anyway, Happy Birthday.

(It’s ok to laugh. Alicia did.) And of course, Alicia and her sister are right.

In Bipolar Disorder: In the Genes? Tina Benitez of FOX News covers the current state of understanding with the following facts:

  • Identical twins have a 70 percent higher chance of developing bipolar disorder.
  • If one parent is bipolar, there is a 7 to 10 percent higher risk of getting bipolar disorder.
  • If there are two parents, there is a 20 percent chance of developing bipolar in the offspring because of the multiple genes.

The Slynar, FAT, and P2RX7 genes are the only three genes thus far to be associated with bipolar disorder.

On a related note, similar to the mania phase of bipolar illness, a person experiencing hypomania is overflowing with energy, ebullience, and excitement. Hypomanic people often accomplish great things and are persuasive leaders. Dr. John Gartner, assistant professor of psychiatry at Johns Hopkins School of Medicine, claims in The Hypomanic Edge that a higher than expected number of Americans are hypomanic, which may be explained by genetics.

America is the land of immigrants and studies have shown that the prevalence of bipolar disorder is higher among this population. In turn, the descendents of these immigrants have a higher risk of hypomania. People affected by bipolar disorder or hypomania may be more willing to risk leaving their home country for a strange, foreign land because they feel invincibile while in their heightened state.

Dr. Kay Redfield Jamison agrees in her book, Exuberance,

Individuals who sought the new, who took risks that others would not, or who rebelled against repressive social systems may have been more likely to immigrate to America and, once there, to succeed.

So perhaps Alicia has a family history of incredible accomplishments but as far as I can tell, she’s done pretty well herself.

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Eye on DNA Headlines for 18 September 2007

by Dr. Hsien-Hsien Lei
Posted September 18, 2007 in Eye on DNA Headlines

  • Kerri Morrone at Six Until Me hosts Grand Rounds 3.52 where she browses the Stop & Blog.
  • The DNA Network welcomes its 28th member – Steve Mount of On Genetics.
  • DNA Direct has a new VP Clinical Affairs, Trisha Brown, and a new Clinical Director, Cynthia Kane. Read more about them in this press release (pdf). (By now you all know I work for them, right?)
  • Nicholas Wade of The New York Times explores moral rules in Is “Do Unto Others” Written Into Our Genes? (HT: Tom Head) Lee Dye wrote a similar article in 2005–Are We Programmed for Kindness?–that mentioned Dr. Philippe Rushton of the University of Western Ontario who conducted a study of 174 pairs of identical twins and 148 pairs of fraternal twins. Results showed that genes account for 42 percent of individual difference in attitudes. But Stanford’s Paul Erlich disagreed:

    Genetic evolution did not determine most of how we act or provide us all with a pre-programmed “human nature.” There is no reason to believe that human beings are either innately violent or innately peaceful, instinctively disposed to wreck their environments or to be conservationists, or born genetically gay or genetically straight.

  • Celera and Merck have teamed up to develop pharmacogenetic tests. Celera will take care of the gene expression assay side of things and Merck will develop diagnostic predictors based on the data for use in clinical trials and other therapeutic uses. (HT: Dr. Bill Koslosky)
  • sweatyThe OR7D4 gene has been linked to people’s perceptions of human body odor (B.O. in common parlance). Two variants of the OR7D4 gene exist; people with one variant thought androstenone–a testosterone-derived steroid found in human urine and sweat–smelled like “old cat pee” while the group with the other variant thought it smelled like “sweet vanilla.” Which group do you think you belong to?

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100 Facts About DNA

by Dr. Hsien-Hsien Lei
Posted August 20, 2007 in DNA Fun, DNA in General

scientist 1I’m on vacation this week but that doesn’t mean Eye on DNA is going to be silent. I’ve prepared posts in advance and figured this list of 100 facts about DNA should keep you busy! It’s not particularly well-organized since I created using stream of consciousness. Ommm.

  1. DNA stands for deoxyribonucleic acid.
  2. DNA is part of our definition of a living organism.
  3. DNA is found in all living things.
  4. DNA was first isolated in 1869 by Friedrich Miescher.
  5. James Watson and Francis Crick figured out the structure of DNA.
  6. DNA is a double helix.
  7. The structure of DNA can be likened to a twisted ladder.
  8. The rungs of the ladder are made up of “bases”
  9. Adenine (A) is a base.
  10. Thymine (T) is a base.
  11. Cytosine (C) is a base
  12. Guanine (G) is a base.
  13. A always pairs with T in DNA.
  14. C also pairs with G in DNA.
  15. The amount of A is equal to the amoun tof T, same for C and G.
  16. A+C = T+G
  17. Hydrogen bonds hold the bases together.
  18. The sides of the DNA ladder is made of sugars and phosphate atoms.
  19. Bases attached to a sugar; this complex is called a nucleoside.
  20. Sugar + phosphate + base = nucleotide.
  21. The DNA ladder usually twists to the right.
  22. There are many conformations of DNA: A-DNA, B-DNA, and Z-DNA are the only ones found in nature.
  23. Almost all the cells in our body have DNA with the exception of red blood cells.
  24. DNA is the “blueprint” of life.
  25. Chromosomal or nuclear DNA is DNA found in the nucleus of cells.
  26. Humans have 46 chromosomes.
  27. Autosomal DNA is part of chromosomal DNA but does not include the two sex chromsomes – X and Y.
  28. One chromosome can have as little as 50 million base pairs or as much as 250 million base pairs.
  29. Mitochondrial DNA (mtDNA) is found in the mitochondria.
  30. mtDNA is only passed from the mother to the child because only eggs have mitochondria, not sperm.
  31. There’s a copy of our entire DNA sequence in every cell of our body with one exception.
  32. Our entire DNA sequence is called a genome.
  33. There’s an estimated 3 billion DNA bases in our genome.
  34. One million bases (called a megabase and abbreviated Mb) of DNA sequence data is roughly equivalent to 1 megabyte of computer data storage space.
  35. Our entire DNA sequence would fill 200 1,000-page New York City telephone directories.
  36. A complete 3 billion base genome would take 3 gigabytes of storage space.
  37. If unwound and tied together, the strands of DNA in one cell would stretch almost six feet but would be only 50 trillionths of an inch wide.
  38. In humans, the DNA molecule in a non-sex cell would have a total length of 1.7 metres.
  39. If you unwrap all the DNA you have in all your cells, you could reach the moon 6000 times!
  40. Our sex cells–eggs and sperm–have only half of our total DNA.
  41. Over 99% of our DNA sequence is the same as other humans’.
  42. DNA can self-replicate using cellular machinery made of proteins.
  43. Genes are made of DNA.
  44. Genes are pieces of DNA passed from parent to offspring that contain hereditary information.
  45. The average gene is 10,000 to 15,000 bases long.
  46. The segment of DNA designated a gene is made up of exons and introns.
  47. Exons have the code for making proteins.
  48. Introns are intervening sequences sometimes called “junk DNA.”
  49. Junk DNA’s function or lack thereof is a source of debate.
  50. Part of “junk DNA” help to regulate the genomic activity.
  51. There are an estimated 20,000 to 25,000 genes in our genome.
  52. In 2000, a rough draft of the human genome (complete DNA sequence) was completed.
  53. In 2003, the final draft of the human genome was completed.
  54. The human genome sequence generated by the private genomics company Celera was based on DNA samples collected from five donors who identified themselves only by race and sex.
  55. If all the DNA in your body was put end to end, it would reach to the sun and back over 600 times (100 trillion times six feet divided by 92 million miles).
  56. It would take a person typing 60 words per minute, eight hours a day, around 50 years to type the human genome.
  57. scientist 09If all three billion letters in the human genome were stacked one millimeter apart, they would reach a height 7,000 times the height of the Empire State Building.
  58. DNA is translated via cellular mechanisms into proteins.
  59. DNA in sets of 3 bases, called a codon, code for amino acids, the building blocks of protein.
  60. Changes in the DNA sequence are called mutations.
  61. Many thing can cause mutations, including UV irradiation from the sun, chemicals like drugs, etc.
  62. Mutations can be changes in just one DNA base.
  63. Mutations can involve more than one DNA base.
  64. Mutations can involve entire segments of chromosomes.
  65. Single nucleotide polymorpshisms (SNPs) are single base changes in DNA.
  66. Short tandem repeats (STRs) are short sequences of DNA repeated consecutively.
  67. Some parts of the DNA sequence do not make proteins.
  68. Genes make up only about 2-3% of our genome.
  69. DNA is affected by the environment; environmental factors can turn genes on and off.
  70. There are many ways you can analyze your DNA using commercially available tests.
  71. Paternity tests compare segments of DNA between the potential father and child.
  72. There are other types of relationship testing that compares DNA between siblings, grandparents and grandchild, etc.
  73. DNA tests can help you understand your risk of disease.
  74. A DNA mutation or variation may be associated with a higher risk of a number of diseases, including breast cancer.
  75. DNA tests can help you understand your family history aka genetic genealogy.
  76. DNA tests can help you understand your ethnic make-up.
  77. DNA can be extracted from many different types of samples: blood, cheek cells, urine.
  78. DNA can be stored either as cells on a cotton swab, buccal brush, or frozen blood or in extracted form.
  79. In forensics, DNA analysis usually looks at 13 specific DNA markers (segments of DNA).
  80. The odds that two individuals will have the same 13-loci DNA profile is about one in one billion.
  81. A DNA fingerprint is a set of DNA markers that is unique for each individual except identical twins.
  82. Identical twins share 100% of their genes.
  83. Siblings share 50% of their genes.
  84. A parent and child share 50% of their genes.
  85. You can extract DNA at home from fruit and even your own cheek cells.
  86. DNA is used to determine the pedigree for livestock or pets.
  87. DNA is used in wildlife forensics to identify endangered species and people who hunt them (poachers).
  88. DNA is used in identify victims of accidents or crime.
  89. DNA is used to exonerate innocent people who’ve been wrongly convicted.
  90. Many countries, including the US and UK, maintain a DNA database of convicted criminals.
  91. The CODIS databank (COmbined DNA Index System) is maintained by the BI and has DNA profiles of convicted criminals.
  92. Polymerase chain reaction (PCR) is used to amplify a sample of DNA so that there are more copies to analyze.
  93. We eat DNA every day.
  94. DNA testing is used to authenticate food like caviar and fine wine.
  95. DNA is used to determine the purity of crops.
  96. Genetically modified crops have DNA from another organism inserted to give the crops properties like pest resistance.
  97. Dolly the cloned sheep had the same nuclear DNA as its donor mom but its mitochondrial DNA came from from the egg mom. (Does that make any sense?)
  98. People like to talk about DNA even if it bears no relation to science or reality.
  99. A group of bloggers who write regularly about DNA and genetics have banded to gether to form The DNA Network.
  100. Lists about DNA can get a little boring.

What do you think I left off the list?

Sources:
Human Molecular Genetics 2
DNA From The Beginning from Cold Spring Harbor
Human Genome Project
NOVA Cracking the Code of Life
Yahoo! Encyclopedia
Molecular Biology Notebook

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Genetic Impossibility: Female Mule Gives Birth to Foal

by Dr. Hsien-Hsien Lei
Posted July 31, 2007 in DNA in General

Pop Quiz: How many chromosomes do humans have? Horses? Donkeys?

Answer: Humans have 46 chromosomes, horses have 64, and donkeys have 62.

mule and horseAlthough that’s an interesting bit of DNA trivia to know, it’s even more interesting in the context of breeding between horses and donkeys. If a horse breeds with a donkey, they end up with sterile offspring that have 63 chrosomes – 32 chromsomes from the horse parent and 31 from from the donkey parent. Horse-donkey offspring aka mules are sterile because their odd number of chromosomes makes it technically difficult for chromosomes to pair up properly during the process of meiosis (cell divison of sperm and eggs). This should mean that mules cannot reproduce.

A female mule in Colorado has beaten insurmountable odds and given birth to a foal . According to Laura and Larry Amos, the owners, there have only been about 50 cases of mules giving birth in the past 200 years and only two have been verified using DNA testing. A previous case of twins born of a mule was made possible by hemiclonal transmission; the father’s chromosomes were silenced and shut down completely. Initial DNA tests on the foal and mother mule-in-question showed that Kate, the female mule, was definitely the mother. Results from a count of the foal’s chromosomes are not yet available. No clue on the possible father.

Mules and More has lots more on Kate and her “Miracle John Mule” including pictures.

HT: Alicia

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Medical Tourism for Preimplantation Genetic Diagnosis (PGD)

by Dr. Hsien-Hsien Lei
Posted July 16, 2007 in DNA Around the World, DNA Testing, DNA and Disease

All parents want to protect their children from harm especially when it comes to serious illnesses. For families who have a history of inherited diseases, there is now the option of preimplantation genetic diagnosis (PGD) where one cell is taken from an early stage embryo and genetically screened for the disease-causing mutation. Currently, PGD can be performed for a long list of diseases including Huntington’s disease, breast cancer, neurofibromatosis, cystic fibrosis, and polycystic kidney disease.

This past weekend, the Brookhyser family was profiled in The Orange County Register. Stacy Brookhyser carries the Huntington’s disease (HD) gene and not only is she destined to develop the disease herself later in life, she has a 50-50 chance of passing on the gene to each child. But with the help of PGD, she and her husband were able to select embryos that are free of the HD gene and now have two healthy twin girls.

twins ultrasound

Last year, a reader in Malaysia, under the pseudonym Rica Lode, contacted me asking for more information on PGD for neurofibromatosis (NF) type I. Here’s what she said about their search for PGD (reprinted here with permission):

I am in my 30s, born and bred in Malaysia. I’ve been married for a few years now with no children yet. I would never imagine one day how genetics would play a strong role in our lives. Genetics, bioethics has never been a part of my vocabulary before until I came across this term, preimplantation genetic diagnosis in the newspapers recently. It appears to be the latest “word” in the world due to “designer babies”. This procedure allows parents to select the gender of their baby effortlessly.

To me and my husband, it’s a God-send solution to our dilemma. Because this procedure ensures we would have a healthy child as it is able to detect genetic disorder. My husband have a genetic disorder condition known as Neurofibromatosis Type I, where benign tumours would grow externally and/ internally on the peripheral nerves. It is a gene mutation on chromosome 17. There’s no known cure. There’s a 50% chance this would passed onto our next of kin.

Rica and her husband searched all over Asia for affordable and available PGD. The situation is much the same in Europe. At the annual meeting of the European Society of Human Reproduction and Embryology, a study on PGD patients travelling abroad for treatment found that patients had the following reasons for searching internationally:

  • PGD was banned in their own country (PGD is banned in Ireland, Switzerland and Germany.)
  • Quality of treatment
  • Test availability
  • Expertise in certain diseases
  • Cost and length of waiting lists in their home countries

According to the study, the situation is untenable for both healthcare providers and patients where free exchange of information is impossible. Doctors are afraid of being prosecuted and patients aren’t able to access all the medical treatment, counselling, and support they need once they leave the country where PGD was performed. Mr. Lawford Davies, a solicitor specialising in reproductive and genetic technologies, recommends that members of the European Union develop a consistent policy across all countries and regulate rather than prohibit PGD. (HT: PHG Foundation)

In the end, elective procedures like PGD will be subject not only to legal restrictions, but also to market forces. Medical tourism is an increasingly lucrative business for the uninsured and the underinsured. There may not be a way around this but at least the procedure is available somewhere somehow.

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