Post by Andrei Tchentchik on Aug 17, 2019 11:49:20 GMT 2
(.#321).- Ata Specimen from Chile, report and Summary by Dr. Garry Nolan.
Ata Specimen from Chile, report and Summary by Dr. Garry Nolan.
NOTE:The DNA research on the specimen is in it's very early stages and incomplete. Much research remains. There is a paradox between initial DNA tests, which are largely computerized data bases, and the clinical findings in X Rays and CAT scans, and Dr. Lachman's conclusion that the specimen is 6 years of age and only 6 inches in length. To date, the DNA data cannot explain these perplexing findings. While human-like, it continues to represent an undefined specimen and a least a year of further genetic analysis will be needed by DNA experts. The un-matched DNA (approximately 2 million base pairs of DNA that are un-matched) will need to be carefully explored, and to date this has not been accomplished.
-Dr. Greer
Chile Specimen
Report and Summary by Dr. Garry Nolan
There is a need to bring modern biomedical, transparent and verifiable analysis to avariety of arenas. In the Fall of 2012 a biomedical analysis was initiated of amummified specimen claimed to have originated in the Atacama Desert of Chile, SouthAmerica. High resolution photographic, X-Ray and Computed Tomography evidencewas taken, along with purification of DNA for whole genome sequence (WGS). The first stage of the study involved analysis by medical experts specializing in pediatricgrowth abnormalities, with primary expertise in the genetics of bone disorders. Theobjective of these initial studies was to rule out, or in, previously known syndromes orrare disorders that could explain the symptoms observed in the specimen. A secondconsideration was to determine the “age at time of death”—given that its size wouldsuggest that the specimen was a pre-term fetus, stillborn, or a deformed post-natalchild. A third, but important, consideration was to determine if the specimen was a non-human hominid such as a South American primate. Morphologic features include that the specimen has only 10 ribs, mild mid facehypoplasia, and shows abnormalities of the skull. The observed abnormalities do notfall into any standard or rare classification of known human pediatric disorders. Asrepresented by a specialist in pediatric human bone and growth disorders (see attachedreport), the 6 inch specimen is a human that was likely 6-8 years of age at the time ofdeath (age based on epiphyseal plate X-Ray density standards). X-Ray imaging andCT scan results confirmed the specimen is biological and is not a non-human primate.
The specimen was concluded by the medical specialist to be a human child with anapparently severe form of dwarfism and other anomalies.To further investigate the specimen, and to determine possible genetic drivers of itsobserved morphology, tissue from the specimen was subjected to whole genomesequencing. 3 milligrams of tissue was used to prepare 12.5 micrograms of purifiedgenomic DNA. The DNA was of high quality, showing little to no serious degradation.DNA was subjected to Illumina library preparation and sequencing on Illumina Miseq(PE250x2), Genome Analyzer IIX (SR36x1), and Hiseq 2000 PE100x2) sequencingplatforms according to manufacturer’s protocols.Over 560 million paired end sequence reads passedautomated quality controlfiltersand provided an estimate 19.6X coverage for the whole genome. Approximately 509million (~91%) reads were mapped to the human reference genome hg19 (providing a17.7 fold coverage of the genome). The presence of ~9% “unmatched” DNA should notbe interpreted to represent anything unusual about the specimen itself. Reasons for thelack of match can include artefacts generated during library preparation, low qualityreads from the instrument, or insufficient data to allow computational alignment againstthe human reference standard. Further, since this sample is likely to be at the least afew decade olds, and possibly older, DNA degradation resulting in apparently “false”mutations can occur. For instance, degradation of cytosine (C) via deamination to uracil(U) would result in false interpretation of a C residue as thymidine (T) and a resultingguanine (G) misread as adenine (A) on the opposite strand.Reconstruction of the mitochondrial DNA sequence and analysis shows an allelefrequency consistent with a B2 haplotype group found on the west coast of SouthAmerica, supporting the claimed origination of the specimen from the Atacama Desertregion of Chile. Sequence analysis definitively rules out the specimen as an example ofa New World primate.Preliminary results demonstrate no statistically relevant alterations of genes encodingproteins commonly associated with known genes for primordial dwarfism or other formsof dwarfism. Therefore, if there is a genetic basis for the symptoms observed in thespecimen the casual mutation(s) are not apparent at this level of resolution and at thisstage of the analysis. As the current list of human disorders is far from complete andmany human disorders are polygenic, there might remain to be found a combination ofmutations working in concert that lead to the observed defect(s).
Next steps : This preliminary report demonstrates how currently available biomedicaltechnologies can be readily applied to the analysis of archeologically andanthropologically relevant human specimens with genetic disorders of unknown origin.
This report is not a formal conclusion on the nature of the mutations or the underlyingcause of the disorder in this human specimen. Currently the data represents(conservatively) a 15 fold whole genome reading and as such is insufficient for definitiveconclusions. Future plans include continued study of this specimen to establish up to a50 fold WHS read that could point to targeted sequencing of hypothetical causalmutations. Comparison of the observed sequence variations against recentlydeveloped ethnically focused genome databases is planned. Full analysis of the DNA,and attempts to link genetics to morphology, will eventually follow in an appropriatelypeer-reviewed article in an accredited scientific journal. The results will beindependently verified before publication.
For preliminary observations by Dr. Garry Nolan.
NOTE : DNA testing is ongoing and not complete.
F I N .
Ata Specimen from Chile, report and Summary by Dr. Garry Nolan.
NOTE:The DNA research on the specimen is in it's very early stages and incomplete. Much research remains. There is a paradox between initial DNA tests, which are largely computerized data bases, and the clinical findings in X Rays and CAT scans, and Dr. Lachman's conclusion that the specimen is 6 years of age and only 6 inches in length. To date, the DNA data cannot explain these perplexing findings. While human-like, it continues to represent an undefined specimen and a least a year of further genetic analysis will be needed by DNA experts. The un-matched DNA (approximately 2 million base pairs of DNA that are un-matched) will need to be carefully explored, and to date this has not been accomplished.
-Dr. Greer
Chile Specimen
Report and Summary by Dr. Garry Nolan
There is a need to bring modern biomedical, transparent and verifiable analysis to avariety of arenas. In the Fall of 2012 a biomedical analysis was initiated of amummified specimen claimed to have originated in the Atacama Desert of Chile, SouthAmerica. High resolution photographic, X-Ray and Computed Tomography evidencewas taken, along with purification of DNA for whole genome sequence (WGS). The first stage of the study involved analysis by medical experts specializing in pediatricgrowth abnormalities, with primary expertise in the genetics of bone disorders. Theobjective of these initial studies was to rule out, or in, previously known syndromes orrare disorders that could explain the symptoms observed in the specimen. A secondconsideration was to determine the “age at time of death”—given that its size wouldsuggest that the specimen was a pre-term fetus, stillborn, or a deformed post-natalchild. A third, but important, consideration was to determine if the specimen was a non-human hominid such as a South American primate. Morphologic features include that the specimen has only 10 ribs, mild mid facehypoplasia, and shows abnormalities of the skull. The observed abnormalities do notfall into any standard or rare classification of known human pediatric disorders. Asrepresented by a specialist in pediatric human bone and growth disorders (see attachedreport), the 6 inch specimen is a human that was likely 6-8 years of age at the time ofdeath (age based on epiphyseal plate X-Ray density standards). X-Ray imaging andCT scan results confirmed the specimen is biological and is not a non-human primate.
The specimen was concluded by the medical specialist to be a human child with anapparently severe form of dwarfism and other anomalies.To further investigate the specimen, and to determine possible genetic drivers of itsobserved morphology, tissue from the specimen was subjected to whole genomesequencing. 3 milligrams of tissue was used to prepare 12.5 micrograms of purifiedgenomic DNA. The DNA was of high quality, showing little to no serious degradation.DNA was subjected to Illumina library preparation and sequencing on Illumina Miseq(PE250x2), Genome Analyzer IIX (SR36x1), and Hiseq 2000 PE100x2) sequencingplatforms according to manufacturer’s protocols.Over 560 million paired end sequence reads passedautomated quality controlfiltersand provided an estimate 19.6X coverage for the whole genome. Approximately 509million (~91%) reads were mapped to the human reference genome hg19 (providing a17.7 fold coverage of the genome). The presence of ~9% “unmatched” DNA should notbe interpreted to represent anything unusual about the specimen itself. Reasons for thelack of match can include artefacts generated during library preparation, low qualityreads from the instrument, or insufficient data to allow computational alignment againstthe human reference standard. Further, since this sample is likely to be at the least afew decade olds, and possibly older, DNA degradation resulting in apparently “false”mutations can occur. For instance, degradation of cytosine (C) via deamination to uracil(U) would result in false interpretation of a C residue as thymidine (T) and a resultingguanine (G) misread as adenine (A) on the opposite strand.Reconstruction of the mitochondrial DNA sequence and analysis shows an allelefrequency consistent with a B2 haplotype group found on the west coast of SouthAmerica, supporting the claimed origination of the specimen from the Atacama Desertregion of Chile. Sequence analysis definitively rules out the specimen as an example ofa New World primate.Preliminary results demonstrate no statistically relevant alterations of genes encodingproteins commonly associated with known genes for primordial dwarfism or other formsof dwarfism. Therefore, if there is a genetic basis for the symptoms observed in thespecimen the casual mutation(s) are not apparent at this level of resolution and at thisstage of the analysis. As the current list of human disorders is far from complete andmany human disorders are polygenic, there might remain to be found a combination ofmutations working in concert that lead to the observed defect(s).
Next steps : This preliminary report demonstrates how currently available biomedicaltechnologies can be readily applied to the analysis of archeologically andanthropologically relevant human specimens with genetic disorders of unknown origin.
This report is not a formal conclusion on the nature of the mutations or the underlyingcause of the disorder in this human specimen. Currently the data represents(conservatively) a 15 fold whole genome reading and as such is insufficient for definitiveconclusions. Future plans include continued study of this specimen to establish up to a50 fold WHS read that could point to targeted sequencing of hypothetical causalmutations. Comparison of the observed sequence variations against recentlydeveloped ethnically focused genome databases is planned. Full analysis of the DNA,and attempts to link genetics to morphology, will eventually follow in an appropriatelypeer-reviewed article in an accredited scientific journal. The results will beindependently verified before publication.
For preliminary observations by Dr. Garry Nolan.
NOTE : DNA testing is ongoing and not complete.
F I N .
