How Accurate is DNA Phasing?

I've been going over the ethnicity result phasing at 23andMe again. My ethnicity results were phased with my mother's because we both tested at 23andMe. These results are also phased even if a parent hasn't tested. Phasing without a parent is done using haplotypes to attempt to separate each chromosome into two parts, one representing each parent. Ancestry also phases results but not for ethnicity. Ancestry phases for the matching process. They use the same haplotype process, however, but don't use parents at all. 

Haplotypes are picked out using computer programs that look for strings of matching alleles in your raw data results. These strings are learned through looking at genomes of those who have tested previously. This is 23andMe's explanation, "The technical term for determining which alleles reside on the same chromosome together is phasing. DNA data like our raw data is called unphased."

Looking at our families 23andMe phased ethnicity results it becomes apparent right away that results phased with at least one parent are much more accurate. Half of the genome can be correctly matched with one parent and anything left over can be attributed to the other parent. 

The breakdown of my ethnicity estimates by parent, below, is correct (they do reflect my documentation and family knowledge. My father's ancestry is about 100% European, whereas my mother had a European father and a mixed heritage Nicaraguan mother). If a parent tests with 23andMe and you connect with them you can get a chart like the one below. 

My ethnicity results vastly improved after they were phased with my mother. I think all of the companies should use phasing. 

A 23andMe explanation of how testing at least one parent can change your results: "Connecting with a parent may also increase the resolution of your assignments. That translates into better Ancestry Composition results, in the sense that you might see more assignment to the fine-resolution ancestries: for example, more Scandinavian and less Broadly Northern European."

Here is an example of how my own results improved. The Chromosome Painting map at 23andMe showed some Native American on the X chromosome I received from my father, which is orange in the illustration below. This was before my mother tested and connected with me. 

Below is the 23andMe X chromosome after my mother tested. The color scheme for Native American has changed and is yellow. The X chromosome I received from my father is now completely British and Irish, which would be correct based on what I know from his X maternal tree. The Native American disappeared. The X chromosome I received from my mother now appears to be nearly completely Native American, which would make sense because more Spanish men originally settled my maternal grandmother's place of origin Nicaragua than women. The chromosomes I received from my mother all moved to the top line of each chromosome which always happens if you phase with a parent.  

Correct Phasing When Phased with Parent

Looking at the Chromosome Painting maps ethnicity results it becomes very apparent that it's phased correctly 99.9% of the time when a parent tests. 

Here we see my Eastern European results which are correctly solely attributed to the chromosome phased as my father's (the bottom line on each chromosome). 

Below you can see my shared segments which mostly match a 1st cousin once removed (some of the segments are also from 2nd and 3rd cousins merged together). We share Austro--Hungarian ancestry on our Kappel/Kapple line. My 1st cousin once removed maternal grandparents and my great-grandparents, were both from the same village on the Austro-Hungarian border. They were mainly ethnically Germanic and Eastern European. If you compare the segments with the ethnicity chart from 23andMe, above, you can see some of  the segments match up very well (the chart below is from Genome Mate Pro and had assigned my father's segment to the top chromosome instead of to the bottom like 23andme).

Here is another view of the 23andMe ethnicity chart showing my French and German segments. They are actually all German segments. Again they match up well between the Kappel matches and the phased ethnicity results. If you look at chromosome 13 below there is an excellent match with the chart above.

When I first DNA tested about 10 years ago I had no German or Eastern European admixture. None of my results represented my grandfather Rudolph Kapple's Austro-Hungarian ancestry; it's very nice to see him represented now. 

Phasing Errors When a Parent hasn't tested

We begin to see problems with phased results that are statistical only with no parent testing. Looking at my cousins' and mother's results who haven't had a parent test you can see phasing errors. 

Below is the 23andMe chart showing my mother's phased ethnicity Chromosome Painting results. You can see where phasing errors occurred. My mother's father was of British Isles and German ancestry with no Native American or Sub Saharan African ancestry. This has been confirmed with both documentation and DNA testing. A paternal first cousin of my mother has DNA tested and has zero Native American or Sub Saharan African. Several of my mother's paternal 1st cousins once removed have also DNA tested and have zero percentages of those admixtures also. There should be no Native American or Sub Saharan segments on my mother's father's chromosomes. Mixing of Native American and British Isles on the same chromosome such as on chromosome 4, chart below, is definitely wrong. The Native American and Sub Saharan are all from my mother's Nicaraguan mother. Nicaraguans are descendants of the Spanish, Native American, and African Slaves that settled the country. 

Below I circled the chromosomes where phasing errors apparently resulted in Native American and African segments to be placed on my mother's father's chromosomes in error. My mother's father's chromosomes can be identified by long stretches of Northern European or British Isles segments. Often my mother's mother's chromosomes are the ones on top, but a few times they have flipped to the bottom one (this has occurred because without a parent testing there is no way to tell for certain which side the chromosome represents). Only 5 chromosomes appear to have phasing errors. 

It appears that some Native American and Sub Saharan African on these chromosomes should either move up to the top or down to the bottom of the chromosome. 

Below is chromosome 4. The top chromosome definitely looks like it would have been from my Nicaraguan grandmother with a couple of stretches of Spanish DNA. So the yellowish Native American should be moved up to the top chromosome, and a chunk of blue broadly European and Spanish should move down. 

Even at 90% confidence level the bottom half of chromosome 4 has a large British Isles segment which definitely represents my mother's father, as you see represented in the blue segment below. That chromosome should be all blue with no Native American. 

I have inherited a segment of Native American DNA in the same region of chromosome 4. This confirms that place on the chromosome is Native American and isn't a false positive result. 

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I don't know what is going on with chromosome 15? A Native American segment overlaps an African segment. The top segment has a long stretch of  blue which is said to be Spanish. The bottom segment has a long stretch of a slightly different shade of blue said to be British Isles. I would guess the tip of 15 is mixed African and Native American , and the African segment should fit somewhere on the top and is definitely related to my mother's mother. I'm not sure what should be on the bottom chromosome once the other segment moves up? 

My own Native American Chromosome Paint chart has the chromosomes accurately phased because my results are not statistically phased but are parentally phased. Only two tiny segments end up on my paternal side chromosomes. This could represent actual very distant Native American ancestry on my father's side? One of his ancestors was an Indian trader in Pennsylvania who did have a Native wife although I'm not sure if we are descended from her? It's also possible that these tiny Native American segments are false positives? In any case the phasing has been at least 98% accurate. My Sub Saharan segments are 100% correct and are all on my Mother's chromosome. 

Analyzing my results along with my mother's and cousins' I can see where phasing with a parent improves DNA results substantially. As more people test new haplotypes will be found which will improve phasing without a parent testing. Otherwise raw data phased for the purpose of matching cousins or ethnicity can sometimes be in error and throw off our results. I am surprised, however, at how often my mother's chromosomes were correctly phased. Only 5 out of the 23 seem to have phasing issues. 

Both my mother and I have DNA that has been placed in the broad categories. It will be interesting to see how much better the phasing becomes and how much of the DNA in the broad categories is eventually correctly identified as more people test. All of the DNA currently assigned to French and German is actually German according to our DNA matches origins. It looks like most of my French DNA is somewhere in the broad European categories? It will be interesting to see if some of the now "European" categorized DNA  is ever named as French?

AncestryDNA claims their phasing process for matching has only a 1% error rate. I'm guessing on an individual level with a mixed genome like mine the error rate would be higher than 1%. Parental and statistical phasing for ethnicity really does improve the estimates. I wish all of the DNA companies would do that. The Chromosome Painting interactive map is an outstanding feature at 23andMe. If you are ethnically mixed, like I am, naming the segments according to ethnicity can help when you compare segments of cousins using chromosome browsers. Accurate ethnicity estimates can help identify the places of origin you share with your DNA matches. GEDmatch has a feature that will allow you to search for matches on each chromosome so you can compare matches with your Chromosome Paint map at 23andMe.

I believe phasing for ethnicity is what makes 23andMe's estimates more accurate than the other companies, especially if a parent also tests. 

Tracing A Black Sheep

 I love Black Sheep ancestors and relatives because they show up in the records more often. Before researching my Grandmother Dorothy Mason-Kapple's family I didn't know anything about the origins of the paternal side of her family? I began tracing the Mason family from scratch a little over 20 years ago. 

I didn't even know what the name of my Grandmother Dorothy's father was? When I located a marriage record for her parents I then discovered his first name was Fred. From there I was able to locate Census records for his parents' household going back to the 1870's. 

I found two children I couldn't place in his widowed Mother Mary Owens-Mason's household in 1900 and 1910. A female name Vera Mason and male named Claude Mason were listed in 1900 as children of Mary E. Mason. I didn't believe that to be correct because of their ages. In 1910 they were listed as Grandchildren which seemed to be more realistic. I couldn't identify whose children they were however. I had thought maybe they were illegitimate children of a daughter because sometimes families covered up illegitimate children by claiming they were the children of their Grandparents. 

It was only last year that I discovered Vera and Claude were half siblings of my Grandmother Dorothy. I didn't know my Grandmother's father had been married before. His first wife died young. In 1900 Fred lived in his mother's household with his children. By 1910 he had married my Great-Grandmother Helen Mullen. His children with his first wife didn't live with this second family. 

My Great-Great Uncle Claude Sylvester Mason turned out to be a black sheep often recorded in newspapers and legal system records. The only family member he seemed to stay in touch with throughout his life was his sister Vera. 

Below is Claude Sylvester Mason's baptismal record from 1898. Oddly his first name Claude was not recorded on it? 

Vera continued to live with her grandmother. Claude was listed with his Grandmother in 1910 but actually lived in the Chicago Parental School, which was a Reform School for truants and incorrigible children.  

One positive thing you can say about this Reform School is it was probably the only integrated school in Chicago at the time. The kids farmed around the facility. The school was run like a military school with children wearing military uniforms and marching around the school grounds. I don't know how long Claude spent in Reform School in Chicago? He spent time there at the age of 11 according to the Census.

Did Reform School reform Claude Mason? No. I can understand, however, why Claude would have strayed from the straight and narrow. His father basically abandoned him. His grandmother Mary struggled financially after her husband died. I'm sure she would have had a difficult time working and managing young children at the same time. Claude probably roamed the notoriously crime ridden streets of some of the poverty stricken South Chicago neighborhoods and picked up bad habits. 

He probably learned more bad habits from fellow inmates at the Reform School. As a Chicago Superintendent of the time Superintendent MacQueary said truants:  "Frequenting cheap theaters, associating with bad companions, smoking, drinking, swearing, drifting into the habits of indolence--he is on the broad highway to crime." Bringing children with bad habits together and removing them from families didn't work when it came to reform either. As the Superintendent also said, "They are the children of the street, and as such are a menace in their possibilities for evil." Most eventually returned to the school after being paroled. 

A year after Claude was recorded at the Parental School his grandmother Mary Owens-Mason died in 1911. I'm not sure who he lived with after that? He was only 12 years old at the time of her death. He returned to Mattoon, Illinois, a previous place the family lived, with his Aunts Ida and Ada for his Grandmother's funeral. His sister Vera also returned with them, but not their father Fred Mason? 

Claude's next brush with the legal system is when he kited checks as a teenager. According to newspaper accounts Claude Mason and accomplice were arrested in Ohio for kiting checks on a crime spree from Chicago to Ohio. Claude had a Great-Uncle who spent some time at a soldier's home in Ohio. Not sure if he went to Ohio to see him? According to newspaper accounts Claude was 19 years old. Actually he was only 17 years old. One article stated his father was a paint dealer which was somewhat accurate. Actually Fred Mason was a painter. According to Claude the boys couldn't afford to live "the high life" in Chicago and that's what prompted the crime spree. He was sentenced to a year in the Ohio State Reformatory where he may have picked up the vocation of Electrician. In 1918 when he registered for the draft his occupation was Electrician. 

After spending a year in the Ohio State Reformatory Claude was in trouble again with the law in 1918. A reformatory didn't reform him this time either. He was arrested for robbery at the National Tea company where he was working. A letter from his sister Vera was intercepted by the Police who were then able to track him down and arrest him.

A few years later Claude is in trouble again. This time he and two others robbed a man on " Lovers' Lane" in Chicago in October of 1921. They were nicknamed the "Lovers' Lane Bandits". 

After the 1921 arrest Claude did some hard time at the notorious Joliet Prison. He served a 4 year sentence at Joliet. 

After his release in 1925 I haven't been able to find any evidence of any trouble with the law until the 1940's. In 1941 Claude was jailed for 60 days in Chicago. He actually relocated to Los Angeles around 1935 where his half siblings Mary, Dorothy, Frank, and Edwin also relocated to after WWII. Apparently he got into some trouble on a visit to Chicago in 1941. 

Unfortunately Claude commits another robbery in Los Angeles and does more hard time at the notorious San Quentin Prison in California. He got 5 years to life. 

 

Claude was scheduled to be paroled in 1948 but was released early in 1945.

According to a description from the San Quentin records Claude had abdominal scars from operations. 

I was happy to find a mug-shot of him with his San Quentin records at Ancestry.com. Although I was saddened to see what a broken man he appeared to be. 

Claude died in 1946, at age 47, soon after his parole from San Quentin. He died in Los Angeles County General Hospital which was a public hospital mainly serving the poor. Patients were generally housed in overcrowded wards.

He died due to Rheumatic Heart disease. He probably had Rheumatic fever as a child. His early death and life of crime are results of his difficult life. His mother died when he was a baby. His father abandoned him. His grandmother Mary Owens-Mason was his guardian. She worked as a washerwoman after the death of her husband Peter Mason and probably didn't have much energy to devote to raising Claude and his sister Vera. Living in poverty in a crime ridden area of Chicago it would have taken a strong person with family support to resist the street gang mentality of South Chicago (street gangs formed around ethnic groups and neighborhoods). If Claude Mason's life had turned out better it would have been a miracle.