Ian, thanks for posting the new samples which appear on GenBank! A completely unrelated question - I sometimes see mutations to some allele different from ACGT like for example TxxxxY - what do these extra letters (like Y) mean? -- Best regards, Atanas Kumbarov http://dna.kumbarov.com/ On 2015-10-18 15:02, Ian Logan via wrote: > List > > A very interesting set of 83 new mtDNA sequences has appeared > on the GenBank database. > > The samples come from cancer samples and accompany the paper > (abstract given below.): > > Lang,M., Vocke,C.D., Merino,M.J., Schmidt,L.S. and Linehan,W.M. > 'Mitochondrial DNA mutations distinguish bilateral multifocal renal > oncocytomas from familial Birt-Hogg-Dube tumors' > Mod. Pathol. 2015 Oct 2 > > The sequences on this post belong to Haplogroups: H, J, K, T, U > > As usual the sequences have been added to my 'Checker' program > to ensure accuracy of transcription. > > As with many mtDNA sequences there are insertions, deletions, > heteroplasmies and fresh mutations. > - but these do appear to be random events. > > It is interesting that there many of the sequences come from uncommon > subgroups - and this makes it diffiluct to know if a 'new' mutation > is indeed 'new' or just a polymorphic result that is not seen very often. > > Ian > ww.ianlogan.co.uk > > ------------------------------- > > Abstract > > Oncocytomas are mostly benign tumors characterized by accumulation of > defective mitochondria, and in sporadic cases, are associated with > disruptive mitochondrial DNA (mtDNA) mutations. However, the role mtDNA > mutations have in renal tumors of Birt-Hogg-Dubé (BHD) patients and > other renal oncocytomas with an apparent genetic component has not been > investigated to date. Here we characterize the mitochondrial genome in > different renal tumors and investigate the possibility of employing > mtDNA sequencing analyses of biopsy specimens to aid in the differential > diagnosis of oncocytomas. The entire mitochondrial genome was sequenced > in 25 samples of bilateral and multifocal (BMF) renal oncocytomas, 30 > renal tumors from BHD patients and 36 non-oncocytic renal tumors of > different histologies as well as in biopsy samples of kidney tumors. > mtDNA sequencing in BMF oncocytomas revealed that all tumors carry > disruptive mutations, which impair the assembly of the NADH-ubiquinone > oxidoreductase. Multiple tumors from a given BMF oncocytoma patient > mainly harbor the same somatic mutation and the kidneys of these > patients display diffuse oncocytosis. In contrast, renal oncocytomas of > patients with BHD syndrome and renal tumors with different histologies > do not show disruptive mtDNA mutations. Moreover, we demonstrate that it > is feasible to amplify and sequence the entire mtDNA in biopsy > specimens, and that these sequences are representative of the tumor DNA. > These results show that pathogenic mtDNA mutations affecting complex I > of the respiratory chain are strongly correlated with the oncocytoma > phenotype in non-BHD-related renal tumors and that mtDNA sequences from > biopsies are predictive of the tumor genotype. This work supports a role > for mtDNA mutations in respiratory chain complexes as diagnostic markers > for renal oncocytomas. > > ---------------- > > KJ801401(cancer-BMF1-1/1) Lang Haplogroup T1a1b 12-OCT-2015 > A73G T152C T195C A263G 315.1C G709A A750G A1438G G1888A A2706G > T4216C A4769G A4917G C7028T G8697A A8860G G9438A T9899C G10143A T10463C > A11251G G11719A A12425- C12633A G13368A C14281T C14766T G14905A G15323A > A15326G > C15452A A15607G G15928A T16126C A16163G C16186T C16188T T16189C C16294T > T16519C > > KJ801402(cancer-BMF1-1/2) Lang Haplogroup T1a1b 12-OCT-2015 > A73G T152C T195C A263G 315.1C G709A A750G A1438G G1888A A2706G > 3571.1C T4216C A4769G A4917G C7028T G8697A A8860G G9438A T9899C G10143A > T10463C A11251G G11719A C12633A G13368A C14281T C14766T G14905A G15323A > A15326G > C15452A A15607G G15928A T16126C A16163G C16186T T16189C C16294T T16519C > > KJ801403(cancer-chRCC12-5) Lang Haplogroup T1a4 12-OCT-2015 > A73G T152C T195C A263G 309.1C 315.1C G709A A750G A1438G G1888A > A2706G T4216C A4769G A4917G A7001G C7028T G8020A A8343G C8465Y G8697A > A8860G G9266A T10463C A11251G G11719A T11776C C12633A G13368A 14623.1C > C14766T > G14905A A15326G C15452A A15607G G15928A T16126C A16163G C16169T C16186T > T16189C > T16263C C16294T T16311C T16519C > > KJ801404(cancer-chRCC12-6) Lang Haplogroup T1a4 12-OCT-2015 > A73G T152C T195C A263G 309.1C 315.1C C549- G709A A750G A1438G > G1888A A2706G T4216C A4769G A4917G A7001G C7028T G8020A A8343G G8697A > A8860G G9266A T10463C A11251G G11719A T11776C C12633A G13368A C14766T > G14905A > A15326G C15452A A15607G G15928A T16126C A16163G C16169T C16186T T16189C > T16263C > C16294T T16311C T16519C > > KJ801405(cancer-chRCC12-3) Lang Haplogroup T1a4 12-OCT-2015 > A73G T152C T195C A263G 309.1C 315.1C G709A A750G A1438G G1888A > A2706G T4216C A4769G A4917G A7001G C7028T G8020A A8343G G8697A A8860G > G9266A T10463C A11251G G11719A T11776C C12633A G13368A C14766T G14905A > A15326G > C15452A A15607G G15928A T16126C A16163G C16169T C16186T T16189C T16263C > C16294T > T16311C T16519C > > KJ801406(cancer-chRCC12-7) Lang Haplogroup T1a4 12-OCT-2015 > A73G T152C T195C A263G 309.1C 315.1C G513A C522- A523- G709A > A750G A1438G G1888A A2706G 3571.1C T4216C A4769G A4917G G5316A A7001G > C7028T G8020A A8343G G8697A A8860G G9266A T10463C A11251G G11719A T11776C > C12633A G13368A C14766T G14905A T15209K A15326G C15452A A15607G G15928A > T16126C > A16163G C16169T C16186T T16189C T16263C C16294T T16311C T16519C > > KJ801407(cancer-chRCC12-8) Lang Haplogroup T1a4 12-OCT-2015 > G71- A73G T152C T195C A263G 309.1C 315.1C G709A A750G A1438G > G1888A A2706G 3571.1C T4216C A4769G A4917G A7001G C7028T G8020A A8343G > G8697A A8860G G9266A T10463C A11251G G11719A T11776C C12633A G13368A > C14766T > G14905A A15326G C15452A A15607G G15928A T16126C A16163G C16169T C16186T > T16189C > T16263C C16294T T16311C T16519C > > KJ801408(cancer-chRCC12-9) Lang Haplogroup T1a4 12-OCT-2015 > A73G T152C T195C A263G 309.1C 315.1C T531C G709A A750G A1438G > G1888A A2706G T4216C A4769G A4917G G6955A A7001G C7028T G8020A A8343G > G8697C A8860G G9266A T10463C A11251G G11719A T11776C C12633A G13368A > C14766T > G14905A A15326G C15452A A15607G G15928A T16126C A16163G C16169T C16186T > T16189C > T16263C C16294T T16311C T16519C > > KJ801409(cancer-BHD2) Lang Haplogroup J1c2 12-OCT-2015 > A73G G185A A188G A263G C295T 309.1C 315.1C C462T T489C A750G > A1438G A2706G G3010A T4216C A4769G C7028T A8860G A10398G A11251G G11719A > A12612G G13708A C14766T T14798C A15326G C15452A C16069T T16126C T16519C > > KJ801410(cancer-VHL3) Lang Haplogroup J1c3g 12-OCT-2015 > A73G G185A A188G A263G C295T 309.1C 315.1C C462T T489C A750G > A1438G A2706G G3010A T4216C A4769G C7028T A8860G G9755A A10398G A11251G > G11719A A12612G G13708A C13934T A14327R C14766T T14798C A15326G C15452A > C16069T > T16126C > > KJ801411(cancer-chRCC4) Lang Haplogroup J1c7a 12-OCT-2015 > A73G G185A G228A A263G C295T 315.1C C462T T489C A750G A1438G > A2706G G3010A T4216C A4769G C6464A C6554T C7028T A8860G A10398G A11251G > G11719A G12127A A12612G A13681G G13708A A14552G C14766T T14798C A15326G > C15452A > C16069T T16092C T16126C C16261T > > KJ801412(cancer-sPAP4) Lang Haplogroup J1c5a1 12-OCT-2015 > A73G G185A G228A A263G C295T 315.1C C462T T489C A750G A1438G > T1535- T2387C A2706G G3010A T4216C A4769G A5198G C7028T A8860G C10192T > A10398G A10598G A11251G T11583Y G11719A A12612G G12895A G13708A C14766T > T14798C > A15326G C15452A C16069T T16126C > > KJ801413(cancer-VHL1) Lang Haplogroup J1b1a1 12-OCT-2015 > A73G T146C C242T A263G C295T 315.1C C462T T489C A750G A1438G > T2158C A2706G G3010A T4216C A4769G G5460A C7028T G8269A G8557A A8860G > A10398G A11251G G11719A G12007A A12612G G13708A T13879C T14470C A14706G > C14766T > A15326G C15452A C16069T T16093C T16126C G16145A T16172C C16222T C16261T > T16362C > > KJ801414(cancer-chRCC2) Lang Haplogroup J2a2b2 12-OCT-2015 > A73G C150T T195C A263G C295T 315.1C C456T T489C A750G A1438G > A2706G T4216C A4769G T6671C C7028T C7476T A8860G G9947A A10398G A10499G > A11002G A11251G G11377A C11698G G11719A A12570G A12612G G12622R T13015C > G13708A > T13830C C14766T G15257A A15326G C15452A A15679G C16069T T16126C A16241G > T16288Y > > KJ801415(cancer-spCC3) Lang Haplogroup J2a1a1 12-OCT-2015 > A73G C150T T152C T195C A215G A263G C295T 315.1C T319C T489C > G513A A750G A1438G A2706G 3571.1C T4216C A4769G C7028T C7476T G7789A > A8860G T10333Y A10398G A10499G A11251G G11377A G11719A A12612G G13708A > A13722G > A14133G C14766T G15257A A15326G C15452A C16069T G16145A T16231C C16261T > T16519C > > KJ801416(cancer-BMF6-1/1) Lang Haplogroup U2e1a1 12-OCT-2015 > A73G T152C T217C A263G 309.1C 315.1C C340T A508G A750G A1438G > G1664A A1811G A2706G C3116T A3720G G4036A A4769G A5390G T5426C C6045T > T6152C C7028T A8860G A10127G A10876G C11197T A11467G G11719A T11732C > A12308G > G12372A T13020C T13734C C14766T A15326G A15907G A16051G G16129C A16182- > A16183- > C16184M T16189C 16193.1C 16193.2C T16362C T16519C > > KJ801417(cancer-BMF6-1/2) Lang Haplogroup U2e1a1 12-OCT-2015 > A73G T152C T217C A263G 309.1C 315.1C C340T A508G 523.1C 523.2A > A750G A1438G A1811G A2706G C3116T A3720G G4036A A4769G A5390G T5426C > C6045T T6152C C7028T A8860G A10127G A10876G C11197T A11467G G11719A T11732C > A12308G G12372A T13020C T13734C C14766T A15326G A15907G A16051G G16129C > A16182- > A16183- C16184M T16189C 16193.1C 16193.2C T16362C T16519C > > KJ801418(cancer-FH2) Lang Haplogroup U2e1e 12-OCT-2015 > A73G T152C T217C A263G 309.1C 315.1C C340T A508G C522- A523- > A750G A1438G A1811G C2526T A2706G A3720G A4769G A5390G T5426C C6045T > T6152C C7028T G8251A A8860G A9926G T10786C A10876G A11467G T11552Y G11719A > A12308G G12372A G12618A T13020C T13734C G14607A C14766T A15326G A15907G > A16051G > G16129C G16145A A16182- A16183- T16189C 16193.1C 16193.2C T16362C T16519C > > KJ801419(cancer- BHD13-1) Lang Haplogroup U4b1b1 12-OCT-2015 > T60C A73G T146C T152C T195C A263G 309.1C 315.1C G499A 523.1C > 523.2A A750G A1438G A1811G A2706G A4547M T4646C A4769G T5999C A6047G > C7028T T7705C A8860G T9047C C11332T T11339C A11467G G11719A A12308G G12372A > A13528G C13565T C14620T C14766T A15326G T15693C T16356C T16519C > > KJ801420(cancer-chRCC7) Lang Haplogroup U4b1a3a 12-OCT-2015 > G69R 71.1G A73G T146C T195C A263G 309.1C 315.1C G499A A750G > A1438G A1811G A2706G A3672G T4646C A4769G A5752- T5999C A6047G C7028T > A7265G T7705C A8860G T9989C T11017C C11332T T11339C A11467G C11674T G11719A > A12308G G12372A C14620T C14766T A15326G T15693C T16356C T16519C > > KJ801421(cancer-BHD9) Lang Haplogroup K1a1a2a 12-OCT-2015 > 71.1G A73G A263G 315.1C C497T A750G T1189C A1438G A1811G A2706G > A3480G T3552C A4769G A6060G C7028T 8276.1C A8860G G9055A T9698C A10398G > A10550G T11299C A11467G G11719A G11914A A12308G G12372A G12771A C14167T > C14766T > T14798C A15326G A15799G G16129A T16224C T16311C T16519C > > KJ801422(cancer-FH4) Lang Haplogroup K1a4a1a2b 12-OCT-2015 > A73G T146C A263G 315.1C C497T A750G T1189C A1438G A1811G A2706G > A3480G A4295G A4769G G6260A C7028T A8860G G9055A A9214G T9698C A10398G > A10550G T11299C A11467G T11485C G11719A C11840T A12308G G12372A T13401C > T13740C > C14167T C14766T T14798C A15326G G15884A T16224C C16245T T16311C T16519C > > KJ801423(cancer-spCC5) Lang Haplogroup K1a-T195C 12-OCT-2015 > A73G T195C A263G 315.1C C497T 523.1C 523.2A 523.3C 523.4A A750G > T1189C A1438G A1811G A2706G A3480G A4769G C7028T A8860G G9055A T9698C > A10398G A10550G T11299C A11467G G11719A A12308G G12372A C14167T C14766T > T14798C > C14997Y A15326G T16093C T16224C T16311C T16519C > > KJ801424(cancer-chrCC6) Lang Haplogroup K1b2a2 12-OCT-2015 > A73G T146C T195C A263G 309.1C 309.2C T310Y 315.1G 523.1C 523.2A > A750G T1189C A1438G A1811G A2706G A3480G A4769G T5021C G5913A C7028T > G7521A A8860G G9055A T9698C A10398G A10550G T11299C A11467G G11719A A12308G > G12372A T12738G G12771A C14167T C14766T T14798C G15045R A15326G T16224C > T16311C > T16519C > > KJ801425(cancer-BHD12) Lang Haplogroup U5b2b4 12-OCT-2015 > A73G C150T G185A A263G C303M 309.1C C311Y 315.1C 315.2C A1438G > C1721T A2706G T3197C A4769G C7028T A7768G A8860G G9477A A9670G A11467G > A11653G G11719A A12308G G12372A A12634G T13617C A13630G A13637G T14182C > C14766T > A15326G T16189C C16193M C16270T T16519C > > KJ801426(cancer-spCC4) Lang Haplogroup H13a1a 12-OCT-2015 > A263G 309.1C 315.1C A750G G811R C858Y A1438G C2259T C2326Y G4201S > A4745G A4769G G6951R A8860G G9755A C13680T C14794Y C14872T A15326G G15927A > > KJ801427(cancer-VHL5) Lang Haplogroup H15a1 12-OCT-2015 > A56T T57C 60.1T A263G 309.1C 309.2C 315.1C A750G A1438G A4769G > T6253C A8860G C10937T T11410C A11821G C14953T A15326G > > KJ801428(cancer-BHD4-4) Lang Haplogroup H5a1 12-OCT-2015 > A235G A263G 315.1C C456T C522- A523- A750G A1438G T4336C A4769G > A8860G T12354C A15326G C15833T T16304C > > > ------------------------------- > To unsubscribe from the list, please send an email to GENEALOGY-DNA-request@rootsweb.com with the word 'unsubscribe' without the 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