On Tuesday, August 29, 2017 at 4:18:06 PM UTC-7, Stewart Baldwin wrote: > Thanks for explaining this.  I knew that they had to do the analysis by > looking at small segments and seeing how they would be attached, but it > hadn't occurred to me that this would make long STRs harder to analyze, > although it is pretty clear now that you mentioned it. I know that the > typical layman probably has a much simpler process in mind, no doubt > aided by all of the CSI-type TV shows where they just put the DNA sample > into a machine, push a button, and presto! (As an expert in the field, > can you even watch those shows without cringing?  There was one such > show recently where the cops had an "expert" genealogist aiding them in > a case, which was so bad it had me shaking my head in disgust.) I think all scientists, and to a lesser extent, all scholars, suffer this. I recall seeing a show doing carbon dating on gold coins. It comes with the territory. In the real world, the tests you see on TV crime shows take 24 hours for the text itself, but the forensic labs always have a queue that is several days long (or, scandalously, in the case of rape kits many years long). > It is > tempting to think of a chromosome as being like a long string of > recording tape that you just put in a device and read from end-to-end, > but I suppose that that technology is still a long way off.  There are several different technologies. The original sequencing approaches would give you a 300 (+/-) bp read from a defined point of your choice. To get the next 300 bp, you had to do another reaction with a new start point toward the end of the previous one, so that you could line them up. Most of the public human genome project was done with a modification of this approach that gave you more like 1000 bp reads from a defined point, but the competing private ones used a completely different approach that produced a whole lot of short (150 bp) pieces and used a computer to line them all up (this is called 'shotgun' sequencing. This approach isn't used any longer, but has been replaced with equivalent techniques that have high-throughput, short read-length. There is a competing technology that does not have this read-length problem - it gives you very long reads (40,000 bp or more), but they have a high error rate, so that approach is good for determining STRs, but has an unacceptable rate of false SNPs. The best result is obtained by coupling the two approaches - use a long-read approach to scaffold the more accurate short-read sequences, but this is rarely done. > Does the > above discussion mean that the "whole" genome sequencing that they talk > about is a misnomer? Yes. As I may have said earlier, when they announced the completion of the human genome 15 years ago, they lied - it still isn't complete, as there are a small number of stretches that have proved completely unobtainable. A 'complete' genome sequence is just shotgun sequencing in which they accumulate enough random sequence as to comprise some multiple of the the total DNA in the organism. A 'complete' genome of a living human will often be in the range of 5- to 10-fold coverage, meaning that if you collect 10 times the total sequence, in 150 bp segments, then statistically speaking you will have covered the vast majority of the genome at least once, and much of it multiple times (which helps catch errors). With ancient DNA, the preservation just isn't that good, and they are usually satisfied with 2-fold coverage, meaning they know they are missing a lot of the variation, but are getting enough of it to do meaningful analysis regardless. > Your comment (elsewhere in this thread) indicating that 23 markers might > not be enough to get good information made me wonder if my own results > are atypical. I was speaking specifically about Richard's, which as reported allow no better assignment than G2, and as I said elsewhere int he thread, G2 had already diverged by 5000 BC, so it is not going to be meaningful. There is a degree of luck involved, as in many cases, 23 markers will catch a distinctive difference that allows a much narrower net to be cast. > Has anybody looked at the list of > names that would pop up if Richard's current STR data was input to > search for all current matches with genetic distance zero on those > markers?  Even if it produces nothing of interest, it still seems worth > a try.  One possible problem is that I am not sure the Promega kit used by the scientists is using the same marker sites as FTDNA uses, but I am unaware of anyone doing further processing of the results. taf