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From: "Ian Logan" <>
Subject: [DNA] New mtDNA LHON sequences from Chinese families
Date: Sat, 13 Nov 2010 09:57:22 -0000


List

11 new mtDNA sequences have appeared on GenBank.

They all come from Chinese subjects with LHON (Leber's Hereditary Optic Neuropathy) and all have the
mutations T14484C.

They come from haplogroups: C4a D5a2a1, D5c, G1a1, G2a1, G2b2, M8a, M10a1a, Y2
and accompany the paper - a free download on:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013426

Mitochondrial DNA sequence variation and haplogroup distribution in Chinese patients with LHON and
m.14484T>C.
Yu D, Jia X, Zhang AM, Li S, Zou Y, Zhang Q, Yao YG.

Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese
Academy of Sciences, Kunming, China.
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Abstract
BACKGROUND: Leber hereditary optic neuropathy (LHON, MIM 535000) is one of the most common
mitochondrial genetic disorders caused by three primary mtDNA mutations (m.3460G>A, m.11778G>A and
m. 14484T>C). The clinical expression of LHON is affected by many additional factors, e.g. mtDNA
background, nuclear genes, and environmental factors. Hitherto, there is no comprehensive study of
Chinese LHON patients with m.14484T>C.

METHODOLOGY/PRINCIPAL FINDINGS: In this study, we analyzed the mtDNA sequence variations and
haplogroup distribution pattern of the largest number of Chinese LHON patients with m.14484T>C to
date. We first determined the complete mtDNA sequences in eleven LHON probands with m.14484T>C, to
discern the potentially pathogenic mutations that co-segregate with m.14484T>C. We then dissected
the matrilineal structure of 52 patients with m.14484T>C (including 14 from unrelated families and
38 sporadic cases) and compared it with the reported Han Chinese from general populations. Complete
mtDNA sequencing showed that the eleven matrilines belonged to nine haplogroups including Y2, C4a,
M8a, M10a1a, G1a1, G2a1, G2b2, D5a2a1, and D5c. We did not identify putatively pathogenic mutation
that was co-segregated with m.14484T>C in these lineages based on the evolutionary analysis.
Compared with the reported Han Chinese from general populations, the LHON patients with m.14484T>C
had significantly higher frequency of haplogroups C, G, M10, and Y, but a lower frequency of
haplogroup F. Intriguingly, we also observed a lower prevalence of F lineages in LHON subjects with
m.11778G>A in our previous study, suggesting that this haplogroup may enact similar role during the
onset of LHON in the presence of m.14484T>C or m.11778G>A.

CONCLUSIONS/SIGNIFICANCE: Our current study provided a comprehensive profile regarding the mtDNA
variation and background of Chinese patients with LHON and m.14484T>C. Matrilineal background might
affect the expression of LHON in Chinese patients with m.14484T>C
-----------

As usual I have added the sequences to my 'Checker' program.

Also, below, for reference I list 14 older GenBank sequences with T14484C - which come from a
variety of haplogroups.
It is of interest that LHON doesn't appear to be linked to clinical LHON in the Western World.

Ian
www.ianlogan.co.uk

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HM460791(LHON) Yu Haplogroup M8a 13-NOV-2010
A73G T146C A263G 315.1C T489C A750G A1438G A2706G A4715G A4769G
C5100T G6179A C7028T A7076G C7196A G8584A C8684T A8701G A8860G C9371T
T9540C A10398G C10400T T10873C G11719A C12705T T13488C T14470C T14484C C14766T
T14783C G15043A G15301A A15326G A15487T T16086C C16184T C16223T T16298C G16319A

HM460792(LHON) Yu Haplogroup G1a1 13-NOV-2010
A73G C150T A263G 315.1C T489C G709A A750G A1438G A2706G T3336C
A4769G A4833G T5108C C7028T C7750T C7867T T8200C A8701G A8860G T9540C
A10398G C10400T T10873C G11719A C12705T T14484C G14569A C14766T T14783C G15043A
G15301A G15323A A15326G A15442G G15497A A15769G A15860G C16223T T16325C T16362C
A16463G T16519C

HM460793(LHON) Yu Haplogroup G2a1 13-NOV-2010
A73G A263G 309.1C 315.1C T489C G709A A750G A1438G A2706G A4769G
A4833G T5108C C5601T C7028T G7600A T8087C A8701G A8860G A9377G T9540C
G9575A A10398G C10400T T10742C T10873C G11719A C12705T A13563G A14071G T14200C
T14484C G14569A C14766T T14783C G15043A G15301A A15326G T16086C G16129A C16223T
C16278T T16362C T16368C G16526A

HM460794(LHON) Yu Haplogroup G2a1 13-NOV-2010
A73G A263G 309.1C 309.2C 315.1C T318C T489C G709A A750G A1438G
A2706G A4769G A4833G T5108C C5601T C7028T G7600A A8701G A8860G A9377G
T9540C G9575A A10398G C10400T T10873C G11719A G12070A C12705T A13563G T14200C
T14484C G14569A C14766T T14783C G15043A G15301A A15326G C16176T C16223T A16227G
C16278T A16293C C16294Y T16362C

HM460795(LHON) Yu Haplogroup D5a2a1 13-NOV-2010
A73G C150T A263G 315.1C T489C A750G C752T T1107C A2581G A2706G
G4491A A4769G C4883T C5178A A5301G C7028T A8701G A8860G A9180G T9540C
A10397G A10398G C10400T T10873C G11719A T11929C T11944C A12026G C12705T T14484C
C14766T T14783C G15043A G15301A A15326G T16092C A16164G T16172C A16182- A16183-
T16189C 16193.1C 16193.2C C16223T C16266T T16311C T16362C

HM460796(LHON) Yu Haplogroup D5a2a1 13-NOV-2010
A73G C150T T152C A263G 309.1C 315.1C T489C C522- A523- G709A
A750G C752T T1107C A2706G A4769G C4883T C5178A A5301G C7028T A8701G
A8860G A9180G T9540C T9977C A10397G A10398G C10400T T10873C G11719A T11944C
A12026G C12705T T13356C T14484C C14766T T14783C G15043A T15191C T15262C G15301A
A15326G T16131A A16164G T16172C A16182- A16183- T16189C 16193.1C 16193.2C C16223T
C16266T T16362C

HM460797(LHON) Yu Haplogroup D5c 13-NOV-2010
A73G C150T C151T T152C A263G 309.1C 309.2C 315.1C T489C A750G
T1107C A1438G A2706G A4200T T4216C A4769G C4883T C5178A A5301G C7028T
A7129G C7669T C8580T A8701G A8860G T9540C A10397G A10398G C10400T T10873C
G11719A T12696C C12705T A12810G T13260C C13984T T14484C C14766T T14783C A14927G
G15043A G15301A A15326G T15622C G15737A 16188.1C 16193.1C C16223T T16311C A16316G
T16356C T16362C

HQ260970(LHON) Yu Haplogroup Y2 13-NOV-2010
A73G A263G 315.1C T482C C522- A523- A644G A750G A1438G A2706G
A4769G A4944G G5147A G5417A T6941C C7028T G7859A G8392A A8860G A10398G
G11719A C12705T T13174C T14178C T14484C A14693G C14766T A14914G A15244G A15326G
T16126C T16231C T16311C

HQ260971(LHON) Yu Haplogroup C4a 13-NOV-2010
A73G A249- A263G 315.1C T489C A750G A1438G 2232.1A A2706G T3552A
A4715G A4769G T5082C C5846T G6026A C7028T C7196A T7999C G8584A A8701G
A8860G T9137C T9540C A9545G A10398G C10400T T10873C G11719A G11914A G11969A
A12672G C12705T A13263G T14318C T14484C C14766T T14783C G15043A T15204C G15301A
A15326G A15487T G16129A C16192T C16223T T16298C C16327T T16519C

HQ260972(LHON) Yu Haplogroup M10a1a 13-NOV-2010
A73G A263G 309.1C 315.1C T489C C522- A523- 573.1C 573.2C 573.3C
G709A A750G A1438G A2706G T3083C 3172.1C A3397G C4140T A4769G C7028T
A7250G C7948T A8701G T8793C G8856A A8860G A9494G T9540C A10398G C10400T
G10646A T10873C G11719A C12549T C12705T G13135A A13152G C14337T T14484C T14502C
C14766T T14783C C15040T G15043A T15071C A15218G G15301A A15326G T16093C G16129A
C16223T T16311C T16357C A16497G

HQ260973(LHON) Yu Haplogroup G2b2 13-NOV-2010
A73G G143A T204C A263G 315.1C T489C G709A A750G A1438G A2706G
A4388G A4769G A4833G T5108C C5601T A6932G C7028T A8701G A8860G T8877C
C9168T T9540C A10398G C10400T T10873C G11719A C12705T A13434G A13563G G13708A
T14484C G14569A C14766T T14783C G15043A G15301A A15326G G15346A G15930A C16223T
C16260T C16291T T16362C T16519C

--------------------

14 other GenBank sequences with T14484C

AP008873 JDsq0055(Japanese) Tanaka Haplogroup [N9a2c] 16-JUL-2005
A73G C150T T195C A263G 309.1C 309.2C 315.1C A750G T961C A1438G A2706G A4769G G5231A G5417A C7028T
A8860G T9750C G10685A G11719A A12358G G12372A C12705T A13857G T14484C C14766T T15067C A15326G
T16172C C16223T C16250T C16257A C16261T

AY195754.2(Caucasian) Mishmar Haplogroup [J1c1] 10-JUN-2004
A73G G185A G228A A263G C295T 309.1C 315.1C C462T T482C T489C A750G A1438G A2706G G3010A T3394C
T4216C A4769G C7028T A8860G A10398G A11251G G11719A A12612G G13708A T14484C C14766T T14798C A15326G
C15452A C16069T T16126C G16213A

AY195778.2(Caucasian) Mishmar Haplogroup [J2b1a3] 10-JUN-2004
A73G C150T T152C A263G C295T 315.1C T489C A750G A1438G A2706G T4216C A4769G C5633T C7028T C7476T
A8860G G10172A A10398G T10966C A11251G G11719A A12612G G13708A T14484C T14488C C14766T G15257A
A15326G C15452A G15812A C16069T T16126C C16193T A16265C C16278T

AY714043(India) Palanichamy Haplogroup [W3a1] 04-OCT-2006
A73G T146C A189G C194T T195C T204C G207A A263G 309.1C 315.1C G709A A750G T1243C T1406C A1438G C2389T
A2706G A3505G A4769G G5046A G5460A C7028T G8251A T8477G A8860G G8994A T10245C C11674T G11719A
A11947G T12414C C12705T A13263G T14484C C14766T A15326G C15490T T15784C G15884C C16223T C16292T
T16297C T16519C

AY882393(Italy) Achilli-Rengo Haplogroup [U8b1] 15-APR-2005
A73G T146C T195C A263G 315.1C C522- A523- A750G A1438G A1811G A2706G G3531A A4769G C6546T A6599G
C7028T A8860G T9012C G9055A T9111C A9324G T9698C G9948A T10084C A11467G G11719A G11914A A12308G
A12358G G12372A G12771A C14167T T14484C C14766T A15326G A16066G G16129A A16183- T16189C 16193.1C
C16234T T16311C T16519C

DQ112719.2(Dominican Rep) Kivisild Haplogroup [L3e1e] 18-OCT-2006
A750G A1438G T2352C A2706G A4769G T5774A T6221C C6587T C7028T A8701G A8860G A9254G T9540C T10370C
A10398G A10819G T10873C C11024T G11719A C12705T A14152G T14212C T14484C G14569A C14766T G15301A
A15326G T15670C T15942C

EF061146(PNG) Friedlaender Haplogroup [Q3b] 28-FEB-2007
A73G A263G 309.1C 315.1C T489C A750G A1438G A2706G T4117C C4335T A4769G G5460A A5843G C7028T A8454G
A8701G G8790A A8860G A9254G T9540C A10398G C10400T A10750G T10873C G11719A G12684A C12705T G12940A
T13500C T14484C C14766T T14783C G15043A G15172A G15301A A15326G G16129A C16223T A16241G T16249C
T16311C T16362C "

EF657594 mtDNA426(Europe) Haplogroup [H3c] 14-JUL-2007
A750G G1211A A1438G A4769G G6261A T6776C G7444A A8860G T12957C G14305A T14484C A15326G

EU431088(Canada) Achilli Haplogroup [D1] 01-AUG-2008
A73G A263G 309.1C 309.2C 315.1C T489C 523.1C 523.2A A750G A1438G C2092T A2706G G3010A A4769G C4883T
C5178A C7028T C8414T A8701G A8860G T9540C A10398G C10400T T10873C G11719A C12705T T14484C C14668T
C14766T T14783C G15043A G15301A A15326G G15930A C16223T T16325C T16362C

EU915478 Pello Haplogroup [J1b1a] 12-DEC-2008
A73G T146C T152C C242T A263G C295T 315.1C C462T T489C A750G T789C A1438G C2025Y T2158C A2706G G3010A
T4216C A4769G G5460A C7028T G8269A G8557A A8860G A10398G G10427A A11251G G11719A G12007A A12612G
G13708A T13743C T13879C T14484C C14766T A15326G C15452A C16069T T16126C G16145A T16172C C16222T
C16261T

EU915479 Pello Haplogroup [J1c2] 12-DEC-2008
A73G G185A A188G A263G C295T 309.1C 315.1C C462T T489C A723R A750G A1438G A2706G G3010A T4216C
A4769G C7028T T7042C C8727T A8860G A10398G A11251G G11719A A12612G G13708A G14279A T14484C C14766T
T14798C A15326G C15452A C16069T T16126C T16362C G16390A

FJ986465 Yang Haplogroup [B4d1] 16-JUN-2009
A73G G185A A189G A263G T489C A750G A827G A1438G A2706G A4769G C7028T C8281- C8282- C8283- C8284-
C8285- T8286- C8287- T8288- A8289- A8860G G10680A G11719A G11914A C13449T A13942G C14239T T14484C
C14766T A15038G A15326G C15535T G15930A T16189C T16217C T16519C

GQ304748 Ghelli Haplogroup [V] 20-DEC-2009
T72C A263G 309.1C 309.2C 315.1C A750G A1438G A2706G G4580A A4769G C7028T A8860G A9254G A9368G G9932A
T14484C A15326G C15904T C16261T T16298C T16519C

GU296566(Czech) Malyarchuk Haplogroup [U5b1b1e] 04-MAY-2010
A73G C150T A263G 315.1C A750G A1438G A2706G T3197C A4769G A5656G C7028T A7385G A7768G T8610C A8860G
G9477A T10927C A11467G G11719A A12308G G12372A G12501A G12618A T13617C G13928A T14182C T14484C
C14766T A15326G T16189C C16192T C16270T


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