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