Currently being updated, John Hagan b1940     

Ignore the introduction and go straight to 23andme

There are many introductions to genetics and this one is suitable except it has many adverts - (I ignore those), and they are from Google:

https://basicbiology.net/biology-101/introduction-to-genetics?amp=1

    Simple human cell

23 human chromosomes in order of size l to 23.
The X and Y, blue background, are the sex chromosomes.
If the pairs are XX the person will be female and XY for males.
The Y chromosomes passes from father to son virtually unchanged.

The above video plays well with Mozilla Firefox browser.

The Human Genome Project

This international project that started in 1990 was completed in 2003 cost nearly 3 thousand million dollars. It produced sequences of about 3 billion DNA base pairs ( A-T or C-G) that make up the human genome and found all of the estimated 20,000 to 25,000 human genes. People who are interested in genealogy may have a male relative´s y-chromosome analysed. For example FTDNA, an American company commercially sequences over 300000 base pairs for private individuals. At each specific location there is a specific nucleotide base, for example A (adenine). However someone may find theirs is T allele. This is a mutation. If 2 or more men have this mutation it is recorded as a SNP (pronounced SNIP); if unique to a single person it is called a novel variant.

There are at least 5 different ways to carry out family history research.

• 1 Paper trails
• 2 Autosomnal DNA testing. This is where strands of chromosomes are compared and matched with other people, male or female.
• 3 For males only, comparing their Y chromosome STRs (short tandem repeats of segmant patterns) with other men
• 4 For males only, comparing their Y chromosome SNP (single nucleotide polymorphism, pronounced SNP). This is a mutation, eg A to T allele, insertion or deletion at a certain position in the molcule.
• 5 For females only, comparing the cell's mitochondria with other people. This is passed from a mother to her children. It mutates very slowly.

My DNA tests

• 23andme test kit
  
• For our Christmas present Chris bought Syvia and me a saliva DNA test kit from the 23andme genotyping provider. Both results arrived before Christmas - mine at the beginning of December and Sylvia's later. It gave the haplogroup from my Y chromosome as R1b1b2a1a2f2, defined by the SNPs (single nucleotide polymorphism) rs11799226 (R-L21) having the allele G: which is a derived allele from the ancestral C: but more importantly rs20321 being R1b-M222 with allele G to A.
  The Y chromosome is passed virtually unaltered from father to son. The R1b-M222 is the most common haplogroup for Northern Ireland: this supports my research that the Benjamin Hagan who lived in Ballybay, County Monaghan and born about 1848 was my great grandfather. Currently much research is being carried out linking surnames to haplogroups. It is possible the O'Hagan clan may be traced back to Ui Neill who lived some 1600 years ago.

The image below shows my genetic relationship with another person. The short coloured lengths show we may be 4th to 5th cousins: more and longer coloured lengths mean closer genetic relationships.



In addition to details of ancestry, DNA relatives, health & wellbeing, family & friends and researct they provide the raw data that can be imported into MS Excel.

• Genetic Health The raw data from 23andme may be linked to other data sites for finding possible genetic risks. Codegen.eu currently carry out this analysis at no cost but state that the information given may be inaccurate, incomplete and it has not been curated by any doctors.



The 23andme raw data may be sent to companies (Codegen below) for analysis of the RS numbers (RSid, relational SNP). It gives a simple estimation then is very detailed. Here is a short extract for rs6314. The actual results have not been given here).

Rheumatoid arthritis risk, rs6314, also known as C1354T or His452Tyr/H452Y, is a SNP in the serotonin 2A receptor HTR2A gene in chromosome 13.
Based on a study of 166 Caucasian patients being treated for depression with paroxetine, rs6314 heterozygotes were associated with better response. There was a significantly higher frequency of heterozygotes in the remitter and response groups in comparison to the non-remitter (odds ratio 7.50, p=0.002) and non-response groups (odds ratio 5.25, p=0.01). rs6314 is part of a 4-SNP haplotype in the serotonin 2A receptor gene HTR2A that has been associated with rheumatoid arthritis in a study of 1800 European patients. The risk allele is rs6314(C). The overall risk for the haplotype CTCC of SNPs rs6311-rs1328674-rs6313-rs6314 is 1.68 (CI: 1.20 - 2.34, p = 0.02). Note: the orientation of rs1328674 in dbSNP is opposite that cited by this publication; therefore, with respect to dbSNP, the haplotype of risk as cited above is CACC rather than CTCC. "Haplotype association analysis suggests that the haplotype CCGCA (at SNPs rs3125, rs6314, rs1923886, rs2224721 and rs2770296) is protective against bipolar disorder (P = 0.021, odds ratio 0.63) and the rarer haplotype CCACG confers risk to the disorder (P = 0.0065, odds ratio 3.08)." Genetic variation in the serotonin 2A receptor and ....much more

 

• FTDNA testing In March 2017 I was tested by FTDNA for 37 STR's (short tanden repeats). From the results they gave my haplogroup as R-M269 (mutation about 7000 to 4000 BC). This was somewhat a disappointment as I knew that we were at least R-M222 (mutation from about 2450BC to 1950BC). My STR results have been compared with other Hagans and the nearest matches so far are 2 GD (genetic difference) meaning that we may have (not too recent) common ancestors.
  
  
• ySEQ.net - y chromosome testing In June 2017 I was tested by ySEQ in Germany for downstream groups below R-M222. I now know that I am at least R-S588 also called FGC4108 (dating from 550AD to 1500AD). I have received some 100 negative SNP results, principally S603 and S7814. They have now given me group S588+ meaning there may be further mutations but they don't test for them yet: this testing is still new and has been reviewed (2020) to R-S588 formed 1850 ybp (years before present) and 1550 yrs, TMRCA (time to the most recent common ancestor) i.e. about 500AD or CE (common era).
  
  
• November 2017 FTDNA often have a Christmas sale. Men who have been tested by FTDNA for STR's (me at Y-DNA STR37, that is they have tested the first 37 short tandem repeats) may take their BigY DNA test. This expensive test sequences about 12 million base pairs. From those results there will be mutations (derived, mutated) and some that that are not (ancestral). The derived results are used to place a person on the haplotree (genetic relationship tree). Also there may be some mutations that have not been found on anyone else (yet). These are called novel variants.
• In addition to Big Y FTDNA has upgraded my SR37 to STR111 for free. A big thank you to them. As mentioned earlier STR's can find family relationships during the last few centuries - especially when linked to family names, and more so for families of Irish descent.
• FTDNA STR-111 results from 5 December 2017
  

  DYS393-13 DYS390-25 DYS19-15 DYS391-11 DYS385-11-13 DYS426-12 DYS388-12 DYS439-13 DYS389I-13 DYS392-14
  DYS389II-29 DYS458-18 DYS459-9-10 DYS455-11 DYS454-11 DYS447-24 DYS437-15 DYS448-18 DYS449-30 DYS464-15-16-16-17
  DYS460-11 Y-GATA-H4-11 YCAII-19-23 DYS456-17 DYS607-15 DYS576-18 DYS570-17 CDY-39-39 DYS442-12 DYS438-12
  DYS531-11 DYS578-9 DYF395S1-15-16 DYS590-8 DYS537-10 DYS641-10 DYS472-8 DYF406S1-10 DYS511-11 DYS425-12
  DYS413-21-23 DYS557-16 DYS594-10 DYS436-12 DYS490-12 DYS534-16 DYS450-8 DYS444-12 DYS481-25 DYS520-20
  DYS446-13 DYS617-12 DYS568-11 DYS487-13 DYS572-11 DYS640-11 DYS492-12 DYS565-12 DYS710-36 DYS485-15
  DYS632-9 DYS495-16 DYS540-12 DYS714-24 DYS716-26 DYS717-19 DYS505-12 DYS556-11 DYS549-12 DYS589-12
  DYS522-11 DYS494-9 DYS533-12 DYS636-12 DYS575-10 DYS638-11 DYS462-11 DYS452-30 DYS445-12 Y-GATA-A10-13
  DYS463-24 DYS441-13 Y-GGAAT-1B07-10 DYS525-10 DYS712-20 DYS593-15 DYS650-19 DYS532-13 DYS715-24 DYS504-17
  DYS513-13 DYS561-15 DYS552-24 DYS726-12 DYS635-23 DYS587-18 DYS643-10 DYS497-14 DYS510-17 DYS434-9 DYS461-12 DYS435-11



• The initial results from the BigY test gave my haplogroup R-S588 but there are also 4 novel variant SNPs that MAY be the same as another male tested.


• On 27 January 2018 I was included on the BigY2 tree (http://ytree.net/DisplayTree.php?blockID=576 ) with 2 other Hagans in an unfinalised haplogroup BY11733 - interesting move forward.


• I am hoping that a (male) descendant from John's other son, John, brother of Benjamin will have a DNA test preferably by FTDNA. Currently I have a number of mutations that are unique to me. If others have the same mutations we may have a new sub-clades (as have the 3 to the left at BY57627, "BY" indicates FTDNA registered the SNP).

References - download pdf and jpg files.
• Family Surnames
• John H haplogroups R-M222 & H13a1a
• The intriguing story of R-M222 - http://www.kennedydna.com
• Ancient O´Neill Clan of Ireland
• My mother: H13a1a story
• Hagan Wikipedia
• Library of Ireland
• Information about Hagan
• Celtic tribes of Ireland
• Wikipedia - La Tène Culture
• Are you descended from king Nialll of the nine hostages?
• HAGINS - HAGENS - O HAGAN Forum (Sept 2001, edited)