Dear Barton, Since you have Family Finder data for your mom (and presumably also for yourself) you have a very simple way to sort this all out. All you need to do is to see which of these 5 people match you on the same segment and which do not. I have previously referred to this as a "poor man's phasing". I summarized this in a message I posted on the ISOGG list on June 4, 2011 as below. I am reposting it here as well. You might also want to read the instructions on doing this that Emily Aulicino and I wrote that may be found at https://dl.dropboxusercontent.com/u/21841126/Basics%20of%20Chromosome%20Mapp ing.docx. The only issue you have to watch for when using this technique is those situations where a crossover has occurred between your mother and you at a specific location. Appropriate chromosome mapping helps you eventually spot these, but if you don't have data from various cousins available for mapping purposes then you will not be able to spot these crossover locations unless you are carefully reviewing all of your matching segment data from your Family Finder and 23andMe matches. I would also suggest you review my mom's match list at https://dl.dropboxusercontent.com/u/21841126/23andMe%20and%20FF%20matches%20 for%20Betty%20Janzen%20(public).xls to see how it is structured. If you didn't have your mom's data, then you would need to ask each of your matches on this particular segment if they match each other in Family Finder in the chromosome browser. If you do that, you need to make sure that the HIR overlaps enough so that it will meet Family Finder's threshold for a match, which is 7.7 cMs. Sincerely, Tim Janzen Let me explain my technique in a little more detail. If you haven't already reviewed my genome map file at http://dl.dropbox.com/u/21841126/chromosome%20map%20Betty%20Janzen.zip, I would suggest that you do so before trying to understand the details. It is important that you note that in that file column G is the chromosome that I received from my mom and that column H is the chromosome that my mom has that she didn't pass on to me. You can delete the data in those columns and then use this file as the file for which you do your analysis of your own data. To start with you need a parent's 23andMe results or Family Finder results and you need one of their children's results. You then need to compile a list of all of the known relatives of the parent who have been tested who are either first cousins to the parent or more distantly related to that parent. If you are using 23andMe data for comparison you then go to the "Family Inheritance: Advanced" section in "Ancestry Labs". You then set the parent as the person whose genome is open in 23andMe by clicking on that name in the drop down menu up at the top of the screen next to "Account". Then set the child as the 2nd optional family member in the "Family Inheritance: Advanced" section. Then select the person to be placed in the "Select a person in question" box. This person needs to be a first cousin or someone else known to be a distant relative of the parent. Then click on "Compare". Then click on "View in a table". This will generate a list of matching segments for both the parent and for the child. If you are comparing data in Family Finder the technique is somewhat different. What I do there is to first log into the parent's account and go to the "Chromosome Browser" section of Family Finder. I then find the relative in the list of matches. I then click on the box next to the relative's name and then click on "Download to Excel". I save the Excel file on my hard drive. I then log into the child's account and go to the "Chromosome Browser" section of Family Finder. I then find the relative in the list of matches. I then click on the box next to the relative's name, click on "Download to Excel", and save the Excel file on my hard drive. I then open both Excel files and copy the data from one Excel file so that it is included right below the data in the other Excel file. I then sort that file by the chromosome and then by start location so that I can see all of the matching segments for both the parent and the child adjacent to each other in the file. I then delete all segments that are under 5 cMs for which the parent and the child do not both share a corresponding matching segment with the relative. It may be reasonable to map some segments in the 3-5 cM range if both the parent and the child share that same segment with the relative but caution is warranted when mapping segments that don't contain at least 700 or more SNPs because some matching segments could be IBS (identical by state) and not IBD (identical by descent). In the Excel file I mentioned above in the first paragraph first fill in the start point in column G with the name of the ancestor that the parent must have received the segment from for all of the segments in which the child also matches the other relative. For example, if a first cousin of the parent is being used for comparison then you would enter into the cell the name of the grandparent of the child who was related to the first cousin in the appropriate cell in the file, the grandparent's year of birth and the name of the relative used for comparison. For instance, if the child's start point was at position 80,000,000 on chromosome 5 then you would fill cell G177752 with the name of the grandparent, their YOB and the name of the relative. Then copy the contents of cell G177752 and drag the contents down to fill in all cells in column G down to the endpoint of that segment. If the end point was at position 104,500,000 then you would fill in the column all the way down to cell G181568. Simultaneously fill in the contents of cells H177752 to H181568 with the name of the spouse of the grandparent and their YOB. I like to add "inf" after the name and the YOB to designate that I have inferred this information from the fact that I have already filled in the corresponding cells in column G. Repeat this same procedure for every segment that the child shares with the relative used for comparison. Once you have done the above then review the segments that the parent shares with the other relative but the child does not. For instance, let's say that the parent's matching segment on chromosome 5 starts at 65,000,000 and continues to 110,000,000. You would then go to cell H174981 and enter the name of the grandparent of the child who was related to the first cousin, their YOB, and the name of the relative used for comparison. I also like to add "inf" after this information to indicate that I inferred the information from the fact that the child doesn't share that matching segment. You would then fill the contents of cell H174981 down to cell H177751 with the same information as is in cell H174981. You would next fill in cells H181569 to H182595 with the same information. This would cover the segment between position 104,500,000 and 110,000,000. I would simultaneously fill in the contents of cells G174981 to H177751 and G181569 to G182595 with the name of the spouse of the grandparent, their YOB, and "inf" after that. In similar fashion continue filling in all the appropriate cells in column H for the segments that the parent shares with the other relative but the child does not and adding the corresponding information for those segments in column G. Once you have recorded the information as recommended for the first relative selected for comparison in the paragraph above then continue in similar fashion for all known relatives who are related no more closely than at the first cousin level of relationship to the parent. If there are segments that multiple relatives share in common with the parent, then I like to modify the contents of the corresponding cells to include the name or the initials of each relative who shares that same segment. This information can be helpful in situations where there is some ambiguity about the start or stop locations for a particular segment. For instance, if you look at my file you will see that in cell G182987 the entry JY1823 Darryl Youngman, FM, and MY. This information continues down to cell G185532. This means that my relatives Darryl Youngman, Frederick Mock, and Mason Youngman all share this segment with both my mom and I. Thus it appears in column G. The ancestor that all 5 of us share in common is Jacob Youngman (b. ca 1823). The segment of DNA just above this segment in the file was shared by Darryl Youngman, Mason Youngman, my mom and me, but not by Frederick Mock. Once you have gone through the comparisons for all of the relatives in your list save it and keep it on hand for reference. When you have a new match in 23andMe compare them in "Family Inheritance: Advanced" section in "Ancestry Labs" to the parent and the child or compare them in Family Finder as I described above. If both the parent, the child, and your new match all share a segment that you have previously mapped in the file you created as described above then you know that the ancestor listed in column G for that particular segment of DNA must have shared ancestry with your new match. If the parent shares a segment in common with your new match, but the child doesn't share that segment with the match then you know that the ancestor listed in column H for that particular segment must have shared ancestry your new match. It is important to bear in mind that small matching segments can be problematic for the purposes of mapping, particularly for data in 23andMe. Let's say for instance that a parent shares a matching segment that is 8 cMs in length with a known second cousin but the child doesn't share that segment. You would thus have mapped that entire segment to column H in your file. However, if by chance there had been a crossover during meiosis in the middle of that segment before a portion of it was passed on to the child then about 4 cMs of the 8 cM segment would be inappropriately mapped to column H when it actually should have been placed in column G. For this reason, I initially started by mapping matching segments that were 10 cMs or longer if a relative shared a segment with the parent but not with the child. If there was a crossover in a segment 10 cMs or longer then the child should have received a segment that was at least 5 cMs in length and would thus show up as a matching segment for the child. One advantage of Family Finder is that FF has a 1 cM threshold for matching segments. If a parent and a child both have a matching segment that is in the 2 to 5 cM range and if the number of matching SNPs is 500 or more then there is a reasonably high likelihood that the matching segment is IBD (identical by descent) and not IBS (identical by state). Another advantage of Family Finder is that Family Finder doesn't round to the nearest millionth base pair like 23andMe does, so there is greater clarity as to the precise boundaries of each matching segment. I have been able to get around the first issue partially and the second issue entirely for 23andMe data by including my family and their relatives in the Mennonite project at http://kquilting.homeserver.com/23andme/index.html where we use a 4 cM threshold for matches and where the matching segments are not rounded to the nearest millionth base pair. Endogamous populations represent another challenging group for mapping purposes since there is a higher likelihood in such populations that matching segments will be IBS (identical by state) and not IBD (identical by descent). In such populations it might be wise to initially start by mapping segments that are at least 10-15 cMs and/or contain greater than 1000 or so SNPs. Phasing data from endogamous populations before doing comparisons is a very good approach and reduces the probability that any particular matching segment will be IBS. Sincerely, Tim -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Barton Lewis Sent: Sunday, September 29, 2013 6:54 PM To: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] ICW - inconsistencies I find the scenarios presented by the ICW feature and the CB difficult to comprehend. I wish I knew what questions to ask my matches (i.e., which of the matches they are or are nor matching). For example, My mother matches A, B, C, D and E on an overlapping segment of chr 20. All are ICW each other, except D is not ICW E and E is not ICW D. All I can glean from this is that my mother is matching D and E on different sides of chr 20. Do I have enough information to tentatively assign the others to a certain side? If not, do I need to be asking each one where they match others on this stretch of chr 20? What is the minimally sufficient information I should request of each of them? Thanks, Barton

Thank you, Tim.  I have not tested myself though I have both parents.  I do not understand how my testing will tell me which side of my mother's genome the five people discussed in my message below fall on, which is the question I am trying to answer.  To the extent I come up as any of these people's matches, I already know which side of my genome they're on - my mom's.  But you so consistently state the importance of a parent-child match that I have decided to go ahead and test.  I hope by doing so and following the steps you outline below I can glean something I have not before. Best, Barton On Sun, Sep 29, 2013 at 11:18 PM, Tim Janzen wrote: > Dear Barton, > Since you have Family Finder data for your mom (and presumably also > for yourself) you have a very simple way to sort this all out. All > you need > to do is to see which of these 5 people match you on the same segment > and > which do not. I have previously referred to this as a "poor man's > phasing". > I summarized this in a message I posted on the ISOGG list on June 4, > 2011 as > below. I am reposting it here as well. You might also want to read > the > instructions on doing this that Emily Aulicino and I wrote that may be > found > at > > https://dl.dropboxusercontent.com/u/21841126/Basics%20of%20Chromosome%20Mapp > ing.docx. The only issue you have to watch for when using this > technique is > those situations where a crossover has occurred between your mother > and you > at a specific location. Appropriate chromosome mapping helps you > eventually > spot these, but if you don't have data from various cousins available > for > mapping purposes then you will not be able to spot these crossover > locations > unless you are carefully reviewing all of your matching segment data > from > your Family Finder and 23andMe matches. I would also suggest you > review my > mom's match list at > > https://dl.dropboxusercontent.com/u/21841126/23andMe%20and%20FF%20matches%20 > for%20Betty%20Janzen%20(public).xls to see how it is structured. If > you > didn't have your mom's data, then you would need to ask each of your > matches > on this particular segment if they match each other in Family Finder > in the > chromosome browser. If you do that, you need to make sure that the > HIR > overlaps enough so that it will meet Family Finder's threshold for a > match, > which is 7.7 cMs. > Sincerely, > Tim Janzen > > Let me explain my technique in a little more detail. If you > haven't > already reviewed my genome map file at > > http://dl.dropbox.com/u/21841126/chromosome%20map%20Betty%20Janzen.zip, > I > would suggest that you do so before trying to understand the details. > It is > important that you note that in that file column G is the chromosome > that I > received from my mom and that column H is the chromosome that my mom > has > that she didn't pass on to me. You can delete the data in those > columns and > then use this file as the file for which you do your analysis of your > own > data. > To start with you need a parent's 23andMe results or Family Finder > results and you need one of their children's results. You then need > to > compile a list of all of the known relatives of the parent who have > been > tested who are either first cousins to the parent or more distantly > related > to that parent. If you are using 23andMe data for comparison you then > go to > the "Family Inheritance: Advanced" section in "Ancestry Labs". You > then set > the parent as the person whose genome is open in 23andMe by clicking > on that > name in the drop down menu up at the top of the screen next to > "Account". > Then set the child as the 2nd optional family member in the "Family > Inheritance: Advanced" section. Then select the person to be placed > in the > "Select a person in question" box. This person needs to be a first > cousin > or someone else known to be a distant relative of the parent. Then > click on > "Compare". Then click on "View in a table". This will generate a > list of > matching segments for both the parent and for the child. If you are > comparing data in Family Finder the technique is somewhat different. > What I > do there is to first log into the parent's account and go to the > "Chromosome > Browser" section of Family Finder. I then find the relative in the > list of > matches. I then click on the box next to the relative's name and then > click > on "Download to Excel". I save the Excel file on my hard drive. I > then log > into the child's account and go to the "Chromosome Browser" section of > Family Finder. I then find the relative in the list of matches. I > then > click on the box next to the relative's name, click on "Download to > Excel", > and save the Excel file on my hard drive. I then open both Excel > files and > copy the data from one Excel file so that it is included right below > the > data in the other Excel file. I then sort that file by the chromosome > and > then by start location so that I can see all of the matching segments > for > both the parent and the child adjacent to each other in the file. I > then > delete all segments that are under 5 cMs for which the parent and the > child > do not both share a corresponding matching segment with the relative. > It > may be reasonable to map some segments in the 3-5 cM range if both the > parent and the child share that same segment with the relative but > caution > is warranted when mapping segments that don't contain at least 700 or > more > SNPs because some matching segments could be IBS (identical by state) > and > not IBD (identical by descent). > In the Excel file I mentioned above in the first paragraph first > fill in > the start point in column G with the name of the ancestor that the > parent > must have received the segment from for all of the segments in which > the > child also matches the other relative. For example, if a first cousin > of > the parent is being used for comparison then you would enter into the > cell > the name of the grandparent of the child who was related to the first > cousin > in the appropriate cell in the file, the grandparent's year of birth > and the > name of the relative used for comparison. For instance, if the > child's > start point was at position 80,000,000 on chromosome 5 then you would > fill > cell G177752 with the name of the grandparent, their YOB and the name > of the > relative. Then copy the contents of cell G177752 and drag the > contents down > to fill in all cells in column G down to the endpoint of that segment. > If > the end point was at position 104,500,000 then you would fill in the > column > all the way down to cell G181568. Simultaneously fill in the contents > of > cells H177752 to H181568 with the name of the spouse of the > grandparent and > their YOB. I like to add "inf" after the name and the YOB to > designate that > I have inferred this information from the fact that I have already > filled in > the corresponding cells in column G. Repeat this same procedure for > every > segment that the child shares with the relative used for comparison. > Once you have done the above then review the segments that the parent > shares with the other relative but the child does not. For instance, > let's > say that the parent's matching segment on chromosome 5 starts at > 65,000,000 > and continues to 110,000,000. You would then go to cell H174981 and > enter > the name of the grandparent of the child who was related to the first > cousin, their YOB, and the name of the relative used for comparison. > I also > like to add "inf" after this information to indicate that I inferred > the > information from the fact that the child doesn't share that matching > segment. You would then fill the contents of cell H174981 down to > cell > H177751 with the same information as is in cell H174981. You would > next > fill in cells H181569 to H182595 with the same information. This > would > cover the segment between position 104,500,000 and 110,000,000. I > would > simultaneously fill in the contents of cells G174981 to H177751 and > G181569 > to G182595 with the name of the spouse of the grandparent, their YOB, > and > "inf" after that. In similar fashion continue filling in all the > appropriate cells in column H for the segments that the parent shares > with > the other relative but the child does not and adding the corresponding > information for those segments in column G. > Once you have recorded the information as recommended for the > first > relative selected for comparison in the paragraph above then continue > in > similar fashion for all known relatives who are related no more > closely than > at the first cousin level of relationship to the parent. If there are > segments that multiple relatives share in common with the parent, then > I > like to modify the contents of the corresponding cells to include the > name > or the initials of each relative who shares that same segment. This > information can be helpful in situations where there is some ambiguity > about > the start or stop locations for a particular segment. For instance, > if you > look at my file you will see that in cell G182987 the entry JY1823 > Darryl > Youngman, FM, and MY. This information continues down to cell > G185532. > This means that my relatives Darryl Youngman, Frederick Mock, and > Mason > Youngman all share this segment with both my mom and I. Thus it > appears in > column G. The ancestor that all 5 of us share in common is Jacob > Youngman > (b. ca 1823). The segment of DNA just above this segment in the file > was > shared by Darryl Youngman, Mason Youngman, my mom and me, but not by > Frederick Mock. > Once you have gone through the comparisons for all of the > relatives in > your list save it and keep it on hand for reference. When you have a > new > match in 23andMe compare them in "Family Inheritance: Advanced" > section in > "Ancestry Labs" to the parent and the child or compare them in Family > Finder > as I described above. If both the parent, the child, and your new > match all > share a segment that you have previously mapped in the file you > created as > described above then you know that the ancestor listed in column G for > that > particular segment of DNA must have shared ancestry with your new > match. If > the parent shares a segment in common with your new match, but the > child > doesn't share that segment with the match then you know that the > ancestor > listed in column H for that particular segment must have shared > ancestry > your new match. > It is important to bear in mind that small matching segments can > be > problematic for the purposes of mapping, particularly for data in > 23andMe. > Let's say for instance that a parent shares a matching segment that is > 8 cMs > in length with a known second cousin but the child doesn't share that > segment. You would thus have mapped that entire segment to column H > in your > file. However, if by chance there had been a crossover during meiosis > in > the middle of that segment before a portion of it was passed on to the > child > then about 4 cMs of the 8 cM segment would be inappropriately mapped > to > column H when it actually should have been placed in column G. For > this > reason, I initially started by mapping matching segments that were 10 > cMs or > longer if a relative shared a segment with the parent but not with the > child. If there was a crossover in a segment 10 cMs or longer then > the > child should have received a segment that was at least 5 cMs in length > and > would thus show up as a matching segment for the child. One advantage > of > Family Finder is that FF has a 1 cM threshold for matching segments. > If a > parent and a child both have a matching segment that is in the 2 to 5 > cM > range and if the number of matching SNPs is 500 or more then there is > a > reasonably high likelihood that the matching segment is IBD (identical > by > descent) and not IBS (identical by state). Another advantage of > Family > Finder is that Family Finder doesn't round to the nearest millionth > base > pair like 23andMe does, so there is greater clarity as to the precise > boundaries of each matching segment. I have been able to get around > the > first issue partially and the second issue entirely for 23andMe data > by > including my family and their relatives in the Mennonite project at > http://kquilting.homeserver.com/23andme/index.html where we use a 4 cM > threshold for matches and where the matching segments are not rounded > to the > nearest millionth base pair. > Endogamous populations represent another challenging group for > mapping > purposes since there is a higher likelihood in such populations that > matching segments will be IBS (identical by state) and not IBD > (identical by > descent). In such populations it might be wise to initially start by > mapping segments that are at least 10-15 cMs and/or contain greater > than > 1000 or so SNPs. Phasing data from endogamous populations before > doing > comparisons is a very good approach and reduces the probability that > any > particular matching segment will be IBS. > Sincerely, > Tim > > -----Original Message----- > From: autosomal-dna-bounces@rootsweb.com > [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of Barton Lewis > Sent: Sunday, September 29, 2013 6:54 PM > To: autosomal-dna@rootsweb.com > Subject: Re: [AUTOSOMAL-DNA] ICW - inconsistencies > > I find the scenarios presented by the ICW feature and the CB difficult > to > comprehend. I wish I knew what questions to ask my matches (i.e., > which of > the matches they are or are nor matching). For example, > > My mother matches A, B, C, D and E on an overlapping segment of chr > 20. All > are ICW each other, except D is not ICW E and E is not ICW D. > All I can glean from this is that my mother is matching D and E on > different > sides of chr 20. Do I have enough information to tentatively assign > the > others to a certain side? If not, do I need to be asking each one > where > they match others on this stretch of chr 20? What is the minimally > sufficient information I should request of each of them? > > Thanks, > > Barton > > > > ______________________________ > For answers to Frequently Asked Questions about mailing lists, please > see: > http://dgmweb.net/MailingListFAQs.html > > > ------------------------------- > To unsubscribe from the list, please send an email to > AUTOSOMAL-DNA-request@rootsweb.com with the word 'unsubscribe' without > the quotes in the subject and the body of the message >

Dear Barton, You received only one of each your mother's paired autosomal chromosomes and likewise for your dad. This basic biological principle allows you to separate your mom's matches into two categories, those who match you as well and those who do not. Assuming that the people who match your mom but don't match you share an HIR with your mom that is IBD (not always a valid assumption, particularly for relatively short HIRs), it may be assumed that anyone who matches your mom, but doesn't match you, is matching your mom on her chromosome that you didn't receive. If you haven't yet carefully scrutinized my mom's match list that I mentioned in my last message, I suggest you do so. In particular, review column J. Life becomes much simpler for an autosomal genetic genealogist when you have data for both parents and yourself in all three of the major genetic genealogy companies' databases. You will never regret having done the Family Finder test yourself once you have your personal! match list available for review. Sincerely, Tim Janzen -----Original Message----- From: autosomal-dna-bounces@rootsweb.com [mailto:autosomal-dna-bounces@rootsweb.com] On Behalf Of BARTON LEWIS Sent: Sunday, September 29, 2013 8:34 PM To: autosomal-dna@rootsweb.com Cc: autosomal-dna@rootsweb.com Subject: Re: [AUTOSOMAL-DNA] ICW - inconsistencies Thank you, Tim. I have not tested myself though I have both parents. I do not understand how my testing will tell me which side of my mother's genome the five people discussed in my message below fall on, which is the question I am trying to answer. To the extent I come up as any of these people's matches, I already know which side of my genome they're on - my mom's. But you so consistently state the importance of a parent-child match that I have decided to go ahead and test. I hope by doing so and following the steps you outline below I can glean something I have not before. Best, Barton

Thanks as always, Tim, for your time and information. Barton On Mon, Sep 30, 2013 at 12:06 AM, Tim Janzen wrote: > Dear Barton, > You received only one of each your mother's paired autosomal > chromosomes and likewise for your dad. This basic biological principle > allows you to separate your mom's matches into two categories, those > who match you as well and those who do not. Assuming that the people > who match your mom but don't match you share an HIR with your mom that > is IBD (not always a valid assumption, particularly for relatively > short HIRs), it may be assumed that anyone who matches your mom, but > doesn't match you, is matching your mom on her chromosome that you > didn't receive. If you haven't yet carefully scrutinized my mom's > match list that I mentioned in my last message, I suggest you do so. > In particular, review column J. Life becomes much simpler for an > autosomal genetic genealogist when you have data for both parents and > yourself in all three of the major genetic genealogy companies' > databases. You will never regret having done the Family Finder test > yourself once you have your personal! > match list available for review. > Sincerely, > Tim Janzen >