The Sasquatch Genome Project: A Failed DNA Study

[hvhart]

Be aware that the Ketchum data is questionable.  More data is needed. 

 

I'm an educator, so I will lead you through this one, hiflier.

 

1.  On http://phylotree.org/resources/rCRS_annotated.htm look up the human mitochondrial genome and locate the mutations found in my book, Table 22.  The phylotree table will show you the mtDNA gene involved and the three base codon which was changed by the mutation.  They are abbreviated in column 3.  Column 4 gives the corresponding AA.

2.  View the table of codons as Table A1 (Appendix A)  in my book.  Locate the particular coden which was mutated and determine which amino acid it changes, if at all since some codons are redundant.

3.  Go to the NCBI website https://www.ncbi.nlm.nih.gov/ and type the accession for rCRS,NC_012920.1, in the search field, with Nucleotide as the database.  

4.  Click "Protein" on the right column of the page and see all the protein sequences for human mtDNA.

5.  Scroll and pick the accession of the protein of interest with the longest sequence (some are partial sequences). CLICK on it.

6.  At the bottom of this protein accession you will find the corresponding protein sequence to the gene you picked in 1.  

7.  Use the short AA abbreviation in Table A1 of my book and the rCRS table in phylotree.org in 1. above to locate the AA affected by the mutation in the overall protein sequence..

8.  Find a reference on this protein structure which indicates the position of the AA found in 1. and see whether it is near the active site and could possibly influence the protein's function.  Congratulations, you are now at the forefront of genetic research.  Good Luck!!

Edited September 3, 2020 by hvhart
reference to original post

[hiflier]

It will take me a while to get up to speed on the methodology you've laid out for answering my questions........but I'm game to learn and will take notes along the way. Thanks for providing some good direction for running this down, "Teach"

Edited September 3, 2020 by hiflier

[hvhart]

20 hours ago, hiflier said:

It will take me a while to get up to speed on the methodology you've laid out for answering my questions........but I'm game to learn and will take notes along the way. Thanks for providing some good direction for running this down, "Teach"

PM me on FB or here with your email and I will arrange to walk you through this on the phone for one mutation to get you started.

[hiflier]

Very kind of you, Dr. Hart. I am certainly interested enough to take you up on that offer. If I may paraphrase an old adage, you could give me the fish but I would be grateful for learning how to catch my own.

Edited September 3, 2020 by hiflier

[Incorrigible1]

Grateful to have Dr. Hart become a contributing member of our humble little bbs.

[hvhart]

51 minutes ago, hiflier said:

Very kind of you, Dr. Hart. I am certainly interested enough to take you up on that offer. If I may paraphrase an old adage, you could give me the fish but I would be grateful for learning how to catch my own.

Precisely the Biblical quote I was thinking of but forgot to post.

I am pleased to share information.  Hopefully, the next time somebody uses bad data to claim a proof of bigfoot DNA they will be met with a barage of science based rebuttals.

[hiflier]

I have often been accused of reading minds. And, like DNA, I experience occurrences in pairs, not threes. I've always poo-pooed the suggestion of being psychic, but as time goes by, and things like our connecting regarding the biblical quote keep happening, I'm wondering if I might have to rethink things. Talk soon.  

Edited September 3, 2020 by hiflier

[hvhart]

On 9/2/2020 at 7:37 PM, hvhart said:

Be aware that the Ketchum data is questionable.  More data is needed. 

 

I'm an educator, so I will lead you through this one, hiflier.

 

1.  On http://phylotree.org/resources/rCRS_annotated.htm look up the human mitochondrial genome and locate the mutations found in my book, Table 22.  The phylotree table will show you the mtDNA gene involved and the three base codon which was changed by the mutation.  They are abbreviated in column 3.  Column 4 gives the corresponding AA.

2.  View the table of codons as Table A1 (Appendix A)  in my book.  Locate the particular codon which was mutated and determine which amino acid it changes, if at all since some codons are redundant.

3.  Go to the NCBI website https://www.ncbi.nlm.nih.gov/ and type the accession for rCRS,NC_012920.1, in the search field, with Nucleotide as the database.  

4.  Click "Protein" on the right column of the page and see all the protein sequences for human mtDNA.

5.  Scroll and pick the accession of the protein of interest with the longest sequence (some are partial sequences). CLICK on it.

6.  At the bottom of this protein accession you will find the corresponding protein sequence to the gene you picked in 1.  

7.  Use the short AA abbreviation in Table A1 of my book and the rCRS table in phylotree.org in 1. above to locate the AA affected by the mutation in the overall protein sequence..

8.  Find a reference on this protein structure which indicates the position of the AA found in 1. and see whether it is near the active site and could possibly influence the protein's function.  Congratulations, you are now at the forefront of genetic research.  Good Luck!!

 

Steps 3. to 7. above are simplified by returning to the rCRS human mitochondrial genome in 1.  and noting the position of the affected AA in the overall protein sequence.  This is in the far right hand column.  .  Remember to convert T in the DNA gene sequence to U in the RNA Codon in my Table A1. Attached is a file of results for the above through step 7 in a table.  Left as an exercise for the student to reproduce/verify this table.

Unusual Extra Mutations.docx

[Outkast]

Received my copy today and having limited understanding of the field, I hope I can keep up...

[hvhart]

4 hours ago, Outkast said:

Received my copy today and having limited understanding of the field, I hope I can keep up...

OK.  Post questions here.

[hiflier]

Is a gene mutation considered a mutation (beyond disease) only if it appears in a haplotype as an outlier? In other words, A gene mutation perhaps wouldn't be seen as a mutation if a certain haplotype always had it? For instance, something in T2B that isn't normally found in, say, H1a/H5e?

 

Or something found in other primates that isn't normally found in Humans? (I get the impression that that's the underlying point of Table 22?)

 

Could you please clarify what the "+" numbers represent in Table 22? Are they the frequency that certain mutations appear, or appear together, in either the GenBank, Phylotree or both?

 

Edited September 6, 2020 by hiflier

[NCBFr]

Dr. Hart -

 

Got my copy a couple of days ago and have made it to page 3 or 4.  I do intend to make it to the end but in the meantime can you please take a crack at my most basic question that I have been asking for almost a decade on this subject.  What would be the results if I sent a real pristine BF tissue sample to a reputable genomics lab understanding that they have no type sample to compare against?  My guess is it would come back as some version of contaminated.  Not sure if I really want to advance the science of BF but if I did, why would I bother with looking for DNA without a body to compare it against?

 

 

 

 

[hvhart]

On 9/6/2020 at 8:21 AM, hiflier said:

Is a gene mutation considered a mutation (beyond disease) only if it appears in a haplotype as an outlier? In other words, A gene mutation perhaps wouldn't be seen as a mutation if a certain haplotype always had it? For instance, something in T2B that isn't normally found in, say, H1a/H5e?

 

Or something found in other primates that isn't normally found in Humans? (I get the impression that that's the underlying point of Table 22?)

 

Could you please clarify what the "+" numbers represent in Table 22? Are they the frequency that certain mutations appear, or appear together, in either the GenBank, Phylotree or both?

 

 

In the basic definition "mutation" means a change in a base.  This can be with respect to a reference system such as rCRS or RSRS (Chapter 11 and http://phylotree.org/), or with respect to a particular genome as a deviant.  It depends on the context.  In the first case there is no implication that the "mutated" form actually came from the reference genome.  In the second case, the implication is that it did.  Table 22 contains extra or "private" mutations that are not part of the haplogroup as represented in phylotree.org.  The plus number is the number of additional extra mutations not specifically listed by base position in this table.  The table would be too big to specify these, and they are not part of the argument of the commonality among certain extra mutations (in the table) and their frequency in other primates (Fig. 27).  Because there were nine of these in S26 that are all found in T2b, I hypothesize that these are from a contamination, e.g. Justin Smeja, the sample's submitter, whose haplogroup is also T2b (Chapter 13).  When there are two or more haplogroups (individuals) in a single sample, you will get mutations (from the reference) from both haplogroups, sometimes one or the other or sometimes both as overlapping electropherogram peaks (Chapter 14).  Table 22 is attached.

[hvhart]

13 hours ago, NCBFr said:

Dr. Hart -

 

Got my copy a couple of days ago and have made it to page 3 or 4.  I do intend to make it to the end but in the meantime can you please take a crack at my most basic question that I have been asking for almost a decade on this subject.  What would be the results if I sent a real pristine BF tissue sample to a reputable genomics lab understanding that they have no type sample to compare against?  My guess is it would come back as some version of contaminated.  Not sure if I really want to advance the science of BF but if I did, why would I bother with looking for DNA without a body to compare it against?

 

 

 

 

 

This is a very good question.  If a universal mammalian primers are used for the HV1 region, cytochrome b, or cytochrome c oxidase 1, you should get the corresponding sequence for these mtDNA regions.  Every effort must be made to decontaminate the sample first, e.g. a hair should be ultrasonicated in water, not vortexed in alcohol/water as Ketchum et al. did.  The sequence can then be compared in BLAST(R) to known sequences AND a phylotree of hits should be constructed (Chapter 7).  Perhaps it matches no species close enough for a species ID, however, its position in the phylotree of hits will tell you what it is most closely related to., human, chimp, other primates, etc.  I did this for Ketchum et al. Samples 26 and 140, and these were in exactly the right places for a black bear and a dog, respectively (Figs. 12, 13 and 14).  Obviously a reference sequence from a sasquatch body part is the "gold standard" here against which all subsequent samples can be compared.  In its absence, however, a phylotree can tell you a lot if you have a pure species sample and use the proper primers.  Researchers who present evidence for a new species make phylotrees from DNA sequences of related species plus their "newbie."  A good example is the Lesula monkey, https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0044271 .  Here the researchers had the new species in hand, however, which is a distinct advantage.  They also presented lots of other evidence for a new species.  Compare this to the ridiculous phylotrees of Ketchum et al.  in Figs 16 and 17, (Chapter 7).  Also, extinct mammals (cave bear, short-faced bear, cave lion and others) plus Denosovans and Neanderthals (a complete genome) were sequenced from small bone fragments amid many contaminants, especially microbes.  Keep reading.  I'm here to help you through it if necessary.    

[hiflier]

43 minutes ago, hvhart said:

....if you have a pure species sample and use the proper primers.

 

This especially has been part of my pursuit on the lab side of things. What I was researching the NOTCH2NL gene for both Great Apes and Humans my hypothesis involved selecting primers that would indicate Great Ape or Human. Now I don't think an assay would need to be anything more than what is already available for either Great Apes or Humans because the assays already exist. What may not exist might be the assays necessary to determine the base pairs in the target gene's alleles themselves. It's why one would need a fresh sample consisting of, say, blood or tissue like a hair tag? Because the chromosomes in a cell nucleus are where gene's are located one needs to have blood or tissue in order to have cells to find genes in.

 

But even if that happens (or not) would the COI (Cox1) be the way to go for species detection? I ask because of this:

 

14 hours ago, NCBFr said:

What would be the results if I sent a real pristine BF tissue sample to a reputable genomics lab understanding that they have no type sample to compare against?

 

 COI seems to be what most scientists and labs are set up to look at for species determination which can be found in mtDNA? Is this where things can go awry? Wouldn't targeting one of the genes specific to Great Apes or Humans be the best hope beyond a body to determine if there is indeed another primate in North America other than Human? I hope I'm not mixing up different issues here. One lab told me it's cheaper to run a test for a single species as opposed to metabarcoding. But might you have a suggestion on something that would definitively determine that odd North American primate? Because this goes to the heart of the DNA or e-DNA method of discovery.